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{ "count": 30618, "next": "?page=2", "previous": null, "list": [ { "name": "Jalview", "description": "Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. 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editing" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://gitlab.jalview.org/jalview/jalview.git", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" }, { "url": "https://www.linkedin.com/company/104771886/", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": "19151095", "pmcid": "PMC2672624", "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "", "date": "2009-05-07T00:00:00Z", "citationCount": 7688, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { 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All rights reserved.Anticancer peptides (ACPs) have emerged as a new class of therapeutic agent for cancer treatment due to their lower toxicity as well as greater efficacy, selectivity and specificity when compared to conventional small molecule drugs. However, the experimental identification of ACPs still remains a time-consuming and expensive endeavor. Therefore, it is desirable to develop and improve upon existing computational models for predicting and characterizing ACPs. In this study, we present a bioinformatics tool called the ACPred, which is an interpretable tool for the prediction and characterization of the anticancer activities of peptides. ACPred was developed by utilizing powerful machine learning models (support vector machine and random forest) and various classes of peptide features. It was observed by a jackknife cross-validation test that ACPred can achieve an overall accuracy of 95.61% in identifying ACPs. In addition, analysis revealed the following distinguishing characteristics that ACPs possess: (i) hydrophobic residue enhances the cationic properties of α-helical ACPs resulting in better cell penetration; (ii) the amphipathic nature of the α-helical structure plays a crucial role in its mechanism of cytotoxicity; and (iii) the formation of disulfide bridges on β-sheets is vital for structural maintenance which correlates with its ability to kill cancer cells. Finally, for the convenience of experimental scientists, the ACPred web server was established and made freely available online.", "date": "2019-01-01T00:00:00Z", "citationCount": 42, "authors": [ { "name": "Schaduangrat N." }, { "name": "Nantasenamat C." }, { "name": "Prachayasittikul V." }, { "name": "Shoombuatong W." } ], "journal": "Molecules" } } ], "credit": [ { "name": "Watshara Shoombuatong", "email": "watshara.sho@mahidol.ac.th", "url": null, "orcidid": "https://orcid.org/0000-0002-3394-8709", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:07:09Z", "lastUpdate": "2025-11-17T12:41:12.905009Z", "editPermission": { "type": "group", "authors": [ "ningning" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LexicMap", "description": "LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes.", "homepage": "https://bioinf.shenwei.me/LexicMap/", "biotoolsID": "lexicmap", "biotoolsCURIE": "biotools:lexicmap", "version": [ "v0.7.0", "v0.6.1", "v0.6.0", "v0.5.0", "v0.4.0", "v0.3.0", "v0.2.0", "v0.1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [], "operatingSystem": [], "language": [ "Other" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/shenwei356/LexicMap", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bioinf.shenwei.me/LexicMap/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2024.08.30.610459", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Wei Shen", "email": "shenwei356@gmail.com", "url": "http://shenwei.me", "orcidid": "https://orcid.org/0000-0002-8099-8258", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "smeds", "additionDate": "2025-06-30T15:03:36.801398Z", "lastUpdate": "2025-11-17T12:41:11.971171Z", "editPermission": { "type": "group", "authors": [ "shenwei356" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "N4 Bias Filter", "description": "The tool is designed to perform image pre-processing to reduce the bias field effect, improving the quality of the image. 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