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{
    "count": 118,
    "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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                        "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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                    "metadata": {
                        "title": "The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote",
                        "abstract": "Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads. © 2013 The Author(s) 2013.",
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                    "metadata": {
                        "title": "SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing",
                        "abstract": "The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. © Copyright 2012, Mary Ann Liebert, Inc.",
                        "date": "2012-05-01T00:00:00Z",
                        "citationCount": 9331,
                        "authors": [
                            {
                                "name": "Bankevich A."
                            },
                            {
                                "name": "Nurk S."
                            },
                            {
                                "name": "Antipov D."
                            },
                            {
                                "name": "Gurevich A.A."
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                            {
                                "name": "Dvorkin M."
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                            {
                                "name": "Kulikov A.S."
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                            {
                                "name": "Lesin V.M."
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                            {
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                            {
                                "name": "Pham S."
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                            {
                                "name": "Prjibelski A.D."
                            },
                            {
                                "name": "Pyshkin A.V."
                            },
                            {
                                "name": "Sirotkin A.V."
                            },
                            {
                                "name": "Vyahhi N."
                            },
                            {
                                "name": "Tesler G."
                            },
                            {
                                "name": "Alekseyev M.A."
                            },
                            {
                                "name": "Pevzner P.A."
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                    "metadata": {
                        "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update",
                        "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.",
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                            {
                                "name": "Afgan E."
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                                "name": "Baker D."
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                                "name": "van den Beek M."
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                            {
                                "name": "Blankenberg D."
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                            {
                                "name": "Bouvier D."
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                            {
                                "name": "Cech M."
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                            {
                                "name": "Chilton J."
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                            {
                                "name": "Clements D."
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                            {
                                "name": "Coraor N."
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                            {
                                "name": "Eberhard C."
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                            {
                                "name": "Gruning B."
                            },
                            {
                                "name": "Guerler A."
                            },
                            {
                                "name": "Hillman-Jackson J."
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                            {
                                "name": "Von Kuster G."
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                            {
                                "name": "Rasche E."
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                            {
                                "name": "Soranzo N."
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                            {
                                "name": "Turaga N."
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                            {
                                "name": "Taylor J."
                            },
                            {
                                "name": "Nekrutenko A."
                            },
                            {
                                "name": "Goecks J."
                            }
                        ],
                        "journal": "Nucleic acids research"
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                    "note": "TopHat can find splice junctions without a reference annotation by mapping RNA-Seq reads to a reference genome. The basename of the genome index to be searched. A list of files containing reads. A list of read alignments Track of junctions reported by TopHat. Tracks of insertions and deletions reported by TopHat.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool"
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                {
                    "uri": "http://edamontology.org/topic_3170",
                    "term": "RNA-Seq"
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                    "term": "Rare diseases"
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                {
                    "doi": "10.1093/bioinformatics/btp120",
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                    "metadata": {
                        "title": "TopHat: Discovering splice junctions with RNA-Seq",
                        "abstract": "Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. © 2009 The Author(s).",
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                        "citationCount": 8085,
                        "authors": [
                            {
                                "name": "Trapnell C."
                            },
                            {
                                "name": "Pachter L."
                            },
                            {
                                "name": "Salzberg S.L."
                            }
                        ],
                        "journal": "Bioinformatics"
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                    "type": [
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            "credit": [
                {
                    "name": "Daehwan Kim",
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        {
            "name": "MUSCLE (EBI)",
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                    "term": "Sequence analysis"
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                    "type": [
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                {
                    "url": "http://www.ebi.ac.uk/Tools/msa/muscle/",
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                    "metadata": {
                        "title": "MUSCLE: Multiple sequence alignment with high accuracy and high throughput",
                        "abstract": "We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5.com/muscle. © Oxford University Press 20004; all rights reserved.",
                        "date": "2004-07-09T00:00:00Z",
                        "citationCount": 25336,
                        "authors": [
                            {
                                "name": "Edgar R.C."
                            }
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                        "journal": "Nucleic Acids Research"
                    }
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        },
        {
            "name": "Clustal 2 (Clustal W, Clustal X)",
            "description": "Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.\nNames occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.",
            "homepage": "http://www.clustal.org/clustal2/",
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                    "type": "rrid",
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            ],
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                            "term": "Multiple sequence alignment"
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                    "input": [
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                                "term": "Sequence"
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                                    "term": "FASTA"
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            ],
            "toolType": [
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                "Desktop application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0084",
                    "term": "Phylogeny"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
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            ],
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                "Windows",
                "Mac"
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                        "Galaxy service"
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                    "note": null
                },
                {
                    "url": "http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal",
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                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "http://www.clustal.org/clustal2/#Download",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                },
                {
                    "url": "https://tracker.debian.org/pkg/clustalw",
                    "type": "Software package",
                    "note": "Debian package (Debian Med Packaging Team). Source code package of the command-line interface Clustal W and the corresponding binary package.",
                    "version": null
                },
                {
                    "url": "https://tracker.debian.org/pkg/clustalx",
                    "type": "Software package",
                    "note": "Debian package (Debian Med Packaging Team). Source code package of the graphical user interface Clustal X and the corresponding binary package.",
                    "version": null
                },
                {
                    "url": "https://bioconda.github.io/recipes/clustalw/README.html",
                    "type": "Software package",
                    "note": "Conda package (Bioconda channel) of the command-line interface Clustal W. Conda recipe at https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clustalw/meta.yaml",
                    "version": null
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            "publication": [
                {
                    "doi": "10.1093/nar/22.22.4673",
                    "pmid": null,
                    "pmcid": "PMC308517",
                    "type": [
                        "Primary"
                    ],
                    "version": "historical CLUSTAL W",
                    "note": "Historical publication on CLUSTAL W. Open access to PDF only.",
                    "metadata": {
                        "title": "CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice",
                        "abstract": "The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available. © 1994 Oxford University Press.",
                        "date": "1994-11-11T00:00:00Z",
                        "citationCount": 52930,
                        "authors": [
                            {
                                "name": "Thompson J.D."
                            },
                            {
                                "name": "Higgins D.G."
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                            {
                                "name": "Gibson T.J."
                            }
                        ],
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                    }
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                {
                    "doi": "10.1093/nar/25.24.4876",
                    "pmid": null,
                    "pmcid": "PMC147148",
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                    "version": "historical CLUSTAL X",
                    "note": "Historical publication on CLUSTAL X. Open access.",
                    "metadata": {
                        "title": "The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools",
                        "abstract": "CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.",
                        "date": "1997-12-15T00:00:00Z",
                        "citationCount": 34092,
                        "authors": [
                            {
                                "name": "Thompson J.D."
                            },
                            {
                                "name": "Gibson T.J."
                            },
                            {
                                "name": "Plewniak F."
                            },
                            {
                                "name": "Jeanmougin F."
                            },
                            {
                                "name": "Higgins D.G."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/bioinformatics/btm404",
                    "pmid": null,
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