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GET /api/t/?outputDataType=%22Sequence%20alignment%22
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{
    "count": 201,
    "next": "?page=2",
    "previous": null,
    "list": [
        {
            "name": "HMMER3",
            "description": "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.",
            "homepage": "http://hmmer.org/",
            "biotoolsID": "hmmer3",
            "biotoolsCURIE": "biotools:hmmer3",
            "version": [
                "3.1b1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "note": "alimask is used to apply a mask line to a multiple sequence alignment, based on provided alignment or model coordinates.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0492",
                            "term": "Multiple sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1916",
                                "term": "Alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
                                }
                            ]
                        }
                    ],
                    "note": "Align sequences to a profile HMM The < hmmfile > should contain only a single profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0296",
                            "term": "Sequence profile generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Construct profile HMM(s) from multiple sequence alignment(s).",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0336",
                            "term": "Format validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3434",
                            "term": "Conversion"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1370",
                                    "term": "HMMER format"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "note": "The hmmconvert utility converts an input profile file to different HMMER formats.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0230",
                            "term": "Sequence generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Sample sequences from a profile HMM.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2422",
                            "term": "Data retrieval"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0968",
                                "term": "Keyword"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Retrieve profile HMM(s) from a file.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1361",
                                "term": "Position frequency matrix"
                            },
                            "format": []
                        }
                    ],
                    "note": "Given an HMM, produce data required to build an HMM logo.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": "Daemon for searching a protein query against a protein database.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0955",
                                "term": "Data index"
                            },
                            "format": []
                        }
                    ],
                    "note": "Prepare an HMM database for hmmscan.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1927",
                                    "term": "EMBL format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1936",
                                    "term": "GenBank format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1963",
                                    "term": "UniProtKB format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0957",
                                "term": "Database metadata"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein profile database. query sequence to search the target database of profiles Needs to have those four auxiliary binary files generated by hmmpress. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search profile(s) against a sequence database. Query profile to search the target database of sequences. Sequence database. Ranked lists of the sequences with the most significant matches to the profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3481",
                            "term": "Probabilistic sequence generation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Collect score distributions on random sequences. The output is a table of numbers, one row for each model. Four different parametric fits to the score data are tested: (1) maximum likelihood fits to both location (mu/tau) and slope (lambda) parameters; (2) assuming lambda=log 2, maximum likelihood fit to the location parameter only; (3) same but assuming an edge- corrected lambda, using current procedures in H3 [Eddy, 2008]; and (4) using both parameters determined by H3s current procedures.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Display summary statistics for a profile file. Tabular file of summary statistics for each profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Iteratively search sequence(s) against a protein database. database sequence The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3494",
                                "term": "DNA sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Build a HMMER binary database file from a sequence file. This binary file may be used as a target database for the DNA search tool nhmmer.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1234",
                                "term": "Sequence set (nucleic acid)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search DNA/RNA queries against a DNA/RNA sequence database. nucleic sequence database",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search nucleotide sequence(s) against collections of nucleotide profiles. The <hmmdb> needs to be pressed using hmmpress before it can be searched with hmmscan. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein sequence database. database of sequences Ranked lists of the sequences with the most significant matches to the query. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0160",
                    "term": "Sequence sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0623",
                    "term": "Gene and protein families"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Perl",
                "C"
            ],
            "license": "Other",
            "collectionID": [
                "HMMER",
                "Animal and Crop Genomics"
            ],
            "maturity": null,
            "cost": null,
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/EddyRivasLab/hmmer",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                },
                {
                    "url": "https://github.com/EddyRivasLab/hmmer/issues",
                    "type": [
                        "Issue tracker"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "HMMER User Guide"
                },
                {
                    "url": "http://hmmer.org/documentation.html",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkr367",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "HMMER web server: Interactive sequence similarity searching",
                        "abstract": "HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s).",
                        "date": "2011-07-01T00:00:00Z",
                        "citationCount": 2484,
                        "authors": [
                            {
                                "name": "Finn R.D."
                            },
                            {
                                "name": "Clements J."
                            },
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1371/journal.pcbi.1002195",
                    "pmid": "22039361",
                    "pmcid": "PMC3197634",
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Accelerated profile HMM searches",
                        "abstract": "Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the \"multiple segment Viterbi\" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call \"sparse rescaling\". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. © 2011 Sean R. Eddy.",
                        "date": "2011-10-01T00:00:00Z",
                        "citationCount": 2414,
                        "authors": [
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "PLoS Computational Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Sean Eddy",
                    "email": "sean@eddylab.org",
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0001-6676-4706",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": {
                "biolib": {
                    "app_name": "hmmsearch",
                    "author_name": "HMMER",
                    "author_username": "HMMER"
                }
            },
            "owner": "ELIXIR-FR",
            "additionDate": "2015-04-03T13:17:38Z",
            "lastUpdate": "2021-10-15T14:09:31.104633Z",
            "editPermission": {
                "type": "group",
                "authors": [
                    "animalandcropgenomics",
                    "laurasansc"
                ]
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "MAFFT",
            "description": "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.",
            "homepage": "http://mafft.cbrc.jp/alignment/server/index.html",
            "biotoolsID": "MAFFT",
            "biotoolsCURIE": "biotools:MAFFT",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0492",
                            "term": "Multiple sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
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                        "title": "MAFFT: Iterative refinement and additional methods",
                        "abstract": "This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then describe recent practical extensions, such as dot plot and adjustment of direction in DNA alignment. We also refer to MUSCLE, another high-performance MSA program. © 2014 Springer Science+Business Media, LLC.",
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                        "authors": [
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                                "name": "Katoh K."
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                                "name": "Standley D.M."
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                        "title": "Parallelization of MAFFT for large-scale multiple sequence alignments",
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                                "name": "Nakamura T."
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                            {
                                "name": "Yamada K.D."
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                            {
                                "name": "Tomii K."
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                                "name": "Katoh K."
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                        "title": "MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization",
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                    "version": "3.0",
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                    "metadata": {
                        "title": "HotSpot Wizard 3.0: Web server for automated design of mutations and smart libraries based on sequence input information",
                        "abstract": "© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools - WHAT-CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.",
                        "date": "2018-07-02T00:00:00Z",
                        "citationCount": 43,
                        "authors": [
                            {
                                "name": "Sumbalova L."
                            },
                            {
                                "name": "Stourac J."
                            },
                            {
                                "name": "Martinek T."
                            },
                            {
                                "name": "Bednar D."
                            },
                            {
                                "name": "Damborsky J."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Jan Stourac",
                    "email": "stourac.jan@gmail.com",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-3139-3700",
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                    "typeEntity": "Person",
                    "typeRole": [
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                        "Support"
                    ],
                    "note": null
                },
                {
                    "name": "Jaroslav Bendl",
                    "email": "jaroslav.bendl@gmail.com",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-9989-2720",
                    "gridid": null,
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                    "typeRole": [
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                },
                {
                    "name": "Lenka Sumbalova",
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                    "url": null,
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                    "typeEntity": "Person",
                    "typeRole": [
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                    ],
                    "note": null
                },
                {
                    "name": "Jan Brezovsky",
                    "email": "brezovsky@mail.muni.cz",
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                    "orcidid": "https://orcid.org/0000-0001-9677-5078",
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                },
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                        "title": "FireProt: web server for automated design of thermostable proteins",
                        "abstract": "© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants.",
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                            {
                                "name": "Musil M."
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                            {
                                "name": "Stourac J."
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                            {
                                "name": "Bendl J."
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                                "name": "Bednar D."
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                            {
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                    "note": "SILVA Incremental Aligner (SINA) is used to align the rRNA gene databases provided by SILVA, as well as user submitted sequences. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. Aligned sequences can be dowloaded as FASTA or ARB files",
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                    "note": "SINA can also operate as a taxonomic classification tool. It uses the search result to derive a classification with the LCA (lowest common ancestor) method. Each query sequence is assigned the shared part of the classifications of the search results. Aligned sequences can be dowloaded as FASTA or ARB files Taxonomic classification results can be downloaded as csv files.",
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                    "note": "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets. TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.",
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                    "note": null,
                    "metadata": {
                        "title": "The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools",
                        "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. © The Author(s) 2012.",
                        "date": "2013-01-01T00:00:00Z",
                        "citationCount": 8390,
                        "authors": [
                            {
                                "name": "Quast C."
                            },
                            {
                                "name": "Pruesse E."
                            },
                            {
                                "name": "Yilmaz P."
                            },
                            {
                                "name": "Gerken J."
                            },
                            {
                                "name": "Schweer T."
                            },
                            {
                                "name": "Yarza P."
                            },
                            {
                                "name": "Peplies J."
                            },
                            {
                                "name": "Glockner F.O."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/nar/gkt1209",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "The SILVA and \"all-species Living Tree Project (LTP)\" taxonomic frameworks",
                        "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources. © 2013 The Author(s). Published by Oxford University Press.",
                        "date": "2014-01-01T00:00:00Z",
                        "citationCount": 890,
                        "authors": [
                            {
                                "name": "Yilmaz P."
                            },
                            {
                                "name": "Parfrey L.W."
                            },
                            {
                                "name": "Yarza P."
                            },
                            {
                                "name": "Gerken J."
                            },
                            {
                                "name": "Pruesse E."
                            },
                            {
                                "name": "Quast C."
                            },
                            {
                                "name": "Schweer T."
                            },
                            {
                                "name": "Peplies J."
                            },
                            {
                                "name": "Ludwig W."
                            },
                            {
                                "name": "Glockner F.O."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/nar/gkm864",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB",
                        "abstract": "Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs. © 2007 The Author(s).",
                        "date": "2007-12-01T00:00:00Z",
                        "citationCount": 3882,
                        "authors": [
                            {
                                "name": "Pruesse E."
                            },
                            {
                                "name": "Quast C."
                            },
                            {
                                "name": "Knittel K."
                            },
                            {
                                "name": "Fuchs B.M."
                            },
                            {
                                "name": "Ludwig W."
                            },
                            {
                                "name": "Peplies J."
                            },
                            {
                                "name": "Glockner F.O."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/bioinformatics/bts252",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes",
                        "abstract": "Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012. Published by Oxford University Press.",
                        "date": "2012-07-01T00:00:00Z",
                        "citationCount": 1704,
                        "authors": [
                            {
                                "name": "Pruesse E."
                            },
                            {
                                "name": "Peplies J."
                            },
                            {
                                "name": "Glockner F.O."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1016/j.jbiotec.2017.06.1198",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Review"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "25 years of serving the community with ribosomal RNA gene reference databases and tools",
                        "abstract": "© 2017 The Author(s)SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.",
                        "date": "2017-11-10T00:00:00Z",
                        "citationCount": 184,
                        "authors": [
                            {
                                "name": "Glockner F.O."
                            },
                            {
                                "name": "Yilmaz P."
                            },
                            {
                                "name": "Quast C."
                            },
                            {
                                "name": "Gerken J."
                            },
                            {
                                "name": "Beccati A."
                            },
                            {
                                "name": "Ciuprina A."
                            },
                            {
                                "name": "Bruns G."
                            },
                            {
                                "name": "Yarza P."
                            },
                            {
                                "name": "Peplies J."
                            },
                            {
                                "name": "Westram R."
                            },
                            {
                                "name": "Ludwig W."
                            }
                        ],
                        "journal": "Journal of Biotechnology"
                    }
                }
            ],
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                    "typeRole": [
                        "Contributor"
                    ],
                    "note": null
                },
                {
                    "name": "Ribocon GmbH",
                    "email": null,
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                    "orcidid": null,
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                    "typeEntity": "Funding agency",
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                        "Contributor"
                    ],
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                },
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