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class="vector-toc-text"> <span class="vector-toc-numb">2</span> <span>See also</span> </div> </a> <ul id="toc-See_also-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#External_links"> <div class="vector-toc-text"> <span class="vector-toc-numb">4</span> <span>External links</span> </div> </a> <ul id="toc-External_links-sublist" class="vector-toc-list"> </ul> </li> </ul> </div> </div> </nav> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header vector-page-titlebar"> <nav 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class="firstHeading mw-first-heading"><span class="mw-page-title-main">EMBOSS</span></h1> <div id="p-lang-btn" class="vector-dropdown mw-portlet mw-portlet-lang" > <input type="checkbox" id="p-lang-btn-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-lang-btn" class="vector-dropdown-checkbox mw-interlanguage-selector" aria-label="Go to an article in another language. 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class="noprint">From Wikipedia, the free encyclopedia</div> </div> <div id="contentSub"><div id="mw-content-subtitle"></div></div> <div id="mw-content-text" class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><div class="shortdescription nomobile noexcerpt noprint searchaux" style="display:none">Open source software analysis package</div> <style data-mw-deduplicate="TemplateStyles:r1236090951">.mw-parser-output .hatnote{font-style:italic}.mw-parser-output div.hatnote{padding-left:1.6em;margin-bottom:0.5em}.mw-parser-output .hatnote i{font-style:normal}.mw-parser-output .hatnote+link+.hatnote{margin-top:-0.5em}@media print{body.ns-0 .mw-parser-output .hatnote{display:none!important}}</style><div role="note" class="hatnote navigation-not-searchable">For other uses, see <a href="/wiki/Embossing_(disambiguation)" class="mw-redirect mw-disambig" title="Embossing (disambiguation)">Embossing (disambiguation)</a>.</div> <style data-mw-deduplicate="TemplateStyles:r1257001546">.mw-parser-output .infobox-subbox{padding:0;border:none;margin:-3px;width:auto;min-width:100%;font-size:100%;clear:none;float:none;background-color:transparent}.mw-parser-output .infobox-3cols-child{margin:auto}.mw-parser-output .infobox .navbar{font-size:100%}@media screen{html.skin-theme-clientpref-night .mw-parser-output .infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .infobox-full-data:not(.notheme) div:not(.notheme){background:#1f1f23!important;color:#f8f9fa}}@media(min-width:640px){body.skin--responsive .mw-parser-output .infobox-table{display:table!important}body.skin--responsive .mw-parser-output .infobox-table>caption{display:table-caption!important}body.skin--responsive .mw-parser-output .infobox-table>tbody{display:table-row-group}body.skin--responsive .mw-parser-output .infobox-table tr{display:table-row!important}body.skin--responsive .mw-parser-output .infobox-table th,body.skin--responsive .mw-parser-output .infobox-table td{padding-left:inherit;padding-right:inherit}}</style><table class="infobox vevent"><caption class="infobox-title summary">EMBOSS</caption><tbody><tr><td colspan="2" class="infobox-image logo"><span class="mw-default-size" typeof="mw:File/Frameless"><a href="/wiki/File:Emboss_logo.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/d/d2/Emboss_logo.jpg/220px-Emboss_logo.jpg" decoding="async" width="220" height="71" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/d/d2/Emboss_logo.jpg 1.5x" data-file-width="300" data-file-height="97" /></a></span></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Written in</th><td class="infobox-data"><a href="/wiki/C_(programming_language)" title="C (programming language)">C</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Available in</th><td class="infobox-data"><a href="/wiki/English_language" title="English language">English</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="/wiki/Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data"><a href="/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a> tool</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="/wiki/Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="/wiki/GNU_General_Public_Licence" class="mw-redirect" title="GNU General Public Licence">GNU General Public Licence</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="http://emboss.open-bio.org">emboss<wbr />.open-bio<wbr />.org</a></span></td></tr></tbody></table> <p><b>EMBOSS</b> is a free c software analysis package developed for the needs of the <a href="/wiki/Molecular_biology" title="Molecular biology">molecular biology</a> and <a href="/wiki/Bioinformatics" title="Bioinformatics">bioinformatics</a> user community.<sup id="cite_ref-Rice2000_1-0" class="reference"><a href="#cite_note-Rice2000-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. </p><p><i>EMBOSS</i> is an acronym for <b>E</b>uropean <b>M</b>olecular <b>B</b>iology <b>O</b>pen <b>S</b>oftware <b>S</b>uite. The <i>European</i> part of the name hints at the wider scope. The core EMBOSS groups are collaborating with many other groups to develop the new applications that the users need. This was done from the beginning with <a href="/wiki/EMBnet" title="EMBnet">EMBnet</a>, the European Molecular Biology Network. EMBnet has many nodes worldwide most of which are national bioinformatics services. EMBnet has the programming expertise. In September 1998, the first workshop was held, when 30 people from EMBnet went to <a href="/wiki/Hinxton" title="Hinxton">Hinxton</a> to learn about EMBOSS and to discuss the way forward.<sup id="cite_ref-Rice1999_2-0" class="reference"><a href="#cite_note-Rice1999-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> </p><p>The EMBOSS package contains a variety of applications for <a href="/wiki/Sequence_alignment" title="Sequence alignment">sequence alignment</a>, rapid database searching with sequence patterns, protein motif identification (including domain analysis), and much more. </p><p>The AJAX and NUCLEUS libraries are released under the <a href="/wiki/GNU_Library_General_Public_Licence" class="mw-redirect" title="GNU Library General Public Licence">GNU Library General Public Licence</a>. EMBOSS applications are released under the <a href="/wiki/GNU_General_Public_Licence" class="mw-redirect" title="GNU General Public Licence">GNU General Public Licence</a>.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="EMBOSS_application_groups">EMBOSS application groups</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=EMBOSS&action=edit&section=1" title="Edit section: EMBOSS application groups"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <table class="wikitable"> <tbody><tr> <th>Group </th> <th>Description </th></tr> <tr> <td>Acd</td> <td>Acd file utilities </td></tr> <tr> <td>Alignment consensus</td> <td>Merging sequences to make a consensus </td></tr> <tr> <td>Alignment differences</td> <td>Finding differences between sequences </td></tr> <tr> <td>Alignment dot plots</td> <td>Dot plot sequence comparisons </td></tr> <tr> <td>Alignment global</td> <td>Global sequence alignment </td></tr> <tr> <td>Alignment local</td> <td>Local sequence alignment </td></tr> <tr> <td>Alignment multiple</td> <td><a href="/wiki/Multiple_sequence_alignment" title="Multiple sequence alignment">Multiple sequence alignment</a> </td></tr> <tr> <td>Display</td> <td>Publication-quality display </td></tr> <tr> <td>Edit</td> <td>Sequence editing </td></tr> <tr> <td>Enzyme kinetics</td> <td>Enzyme kinetics calculations </td></tr> <tr> <td>Feature tables</td> <td>Manipulation and display of sequence annotation </td></tr> <tr> <td>HMM</td> <td>Hidden markov model analysis </td></tr> <tr> <td>Information</td> <td>Information and general help for users </td></tr> <tr> <td>Menus</td> <td>Menu interface(s) </td></tr> <tr> <td>Nucleic 2d structure</td> <td>Nucleic acid secondary structure </td></tr> <tr> <td>Nucleic codon usage</td> <td>Codon usage analysis </td></tr> <tr> <td>Nucleic composition</td> <td>Composition of nucleotide sequences </td></tr> <tr> <td>Nucleic CpG islands</td> <td>CpG island detection and analysis </td></tr> <tr> <td>Nucleic gene finding</td> <td>Predictions of genes and other genomic features </td></tr> <tr> <td>Nucleic motifs</td> <td>Nucleic acid motif searches </td></tr> <tr> <td>Nucleic mutation</td> <td>Nucleic acid sequence mutation </td></tr> <tr> <td>Nucleic primers</td> <td>Primer prediction </td></tr> <tr> <td>Nucleic profiles</td> <td>Nucleic acid profile generation and searching </td></tr> <tr> <td>Nucleic repeats</td> <td>Nucleic acid repeat detection </td></tr> <tr> <td>Nucleic restriction</td> <td>Restriction enzyme sites in nucleotide sequences </td></tr> <tr> <td>Nucleic RNA folding</td> <td>RNA folding methods and analysis </td></tr> <tr> <td>Nucleic transcription</td> <td>Transcription factors, promoters and terminator prediction </td></tr> <tr> <td>Nucleic translation</td> <td>Translation of nucleotide sequence to protein sequence </td></tr> <tr> <td>Phylogeny consensus</td> <td>Phylogenetic consensus methods </td></tr> <tr> <td>Phylogeny continuous characters</td> <td>Phylogenetic continuous character methods </td></tr> <tr> <td>Phylogeny discrete characters</td> <td>Phylogenetic discrete character methods </td></tr> <tr> <td>Phylogeny distance matrix</td> <td>Phylogenetic distance matrix methods </td></tr> <tr> <td>Phylogeny gene frequencies</td> <td>Phylogenetic gene frequency methods </td></tr> <tr> <td>Phylogeny molecular sequence</td> <td>Phylogenetic molecular sequence methods </td></tr> <tr> <td>Phylogeny tree drawing</td> <td>Phylogenetic tree drawing methods </td></tr> <tr> <td>Protein 2d structure</td> <td>Protein secondary structure </td></tr> <tr> <td>Protein 3d structure</td> <td>Protein tertiary structure </td></tr> <tr> <td>Protein composition</td> <td>Composition of protein sequences </td></tr> <tr> <td>Protein motifs</td> <td>Protein motif searches </td></tr> <tr> <td>Protein mutation</td> <td>Protein sequence mutation </td></tr> <tr> <td>Protein profiles</td> <td>Protein profile generation and searching </td></tr> <tr> <td>Test</td> <td>Testing tools, not for general use </td></tr> <tr> <td>Utils database creation</td> <td>Database installation </td></tr> <tr> <td>Utils database indexing</td> <td>Database indexing </td></tr> <tr> <td>Utils misc</td> <td>Utility tools </td></tr></tbody></table> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=EMBOSS&action=edit&section=2" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><a href="/wiki/Open_Bioinformatics_Foundation" title="Open Bioinformatics Foundation">Open Bioinformatics Foundation</a></li> <li>Soaplab - A <a href="/wiki/SOAP_(protocol)" class="mw-redirect" title="SOAP (protocol)">SOAP</a> web service interface including EMBOSS</li> <li><a href="/wiki/Genostar" title="Genostar">Genostar</a> - Integration of some of EMBOSS tools in a graphical application</li></ul> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=EMBOSS&action=edit&section=3" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist"> <div class="mw-references-wrap"><ol class="references"> <li id="cite_note-Rice2000-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-Rice2000_1-0">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFRiceLongdenBleasby2000" class="citation journal cs1">Rice P, Longden I, Bleasby A (2000). "EMBOSS: The European Molecular Biology Open Software Suite". <i>Trends in Genetics</i>. <b>16</b> (6): 276–277. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2FS0168-9525%2800%2902024-2">10.1016/S0168-9525(00)02024-2</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/10827456">10827456</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Trends+in+Genetics&rft.atitle=EMBOSS%3A+The+European+Molecular+Biology+Open+Software+Suite&rft.volume=16&rft.issue=6&rft.pages=276-277&rft.date=2000&rft_id=info%3Adoi%2F10.1016%2FS0168-9525%2800%2902024-2&rft_id=info%3Apmid%2F10827456&rft.aulast=Rice&rft.aufirst=P&rft.au=Longden%2C+I&rft.au=Bleasby%2C+A&rfr_id=info%3Asid%2Fen.wikipedia.org%3AEMBOSS" class="Z3988"></span></span> </li> <li id="cite_note-Rice1999-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-Rice1999_2-0">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRiceBleasby1999" class="citation journal cs1">Rice P, Bleasby A (1999). <a rel="nofollow" class="external text" href="http://www.biochemist.org/bio/cyber/9910/default.htm">"EMBOSS: The European Molecular Biology Open Software Suite"</a>. <i>Biochemist E-volution</i>. <b>16</b> (6): 276–7. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fs0168-9525%2800%2902024-2">10.1016/s0168-9525(00)02024-2</a>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/10827456">10827456</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Biochemist+E-volution&rft.atitle=EMBOSS%3A+The+European+Molecular+Biology+Open+Software+Suite&rft.volume=16&rft.issue=6&rft.pages=276-7&rft.date=1999&rft_id=info%3Adoi%2F10.1016%2Fs0168-9525%2800%2902024-2&rft_id=info%3Apmid%2F10827456&rft.aulast=Rice&rft.aufirst=P&rft.au=Bleasby%2C+A&rft_id=http%3A%2F%2Fwww.biochemist.org%2Fbio%2Fcyber%2F9910%2Fdefault.htm&rfr_id=info%3Asid%2Fen.wikipedia.org%3AEMBOSS" class="Z3988"></span></span> </li> <li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://emboss.open-bio.org/html/dev/ch01s01.html">"1.1. Licence Information"</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=1.1.+Licence+Information&rft_id=http%3A%2F%2Femboss.open-bio.org%2Fhtml%2Fdev%2Fch01s01.html&rfr_id=info%3Asid%2Fen.wikipedia.org%3AEMBOSS" class="Z3988"></span></span> </li> </ol></div></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=EMBOSS&action=edit&section=4" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li><span class="official-website"><span class="url"><a rel="nofollow" class="external text" href="http://emboss.open-bio.org">Official website</a></span></span></li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output 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.navbar{display:none!important}}</style><div class="navbar plainlinks hlist navbar-mini"><ul><li class="nv-view"><a href="/wiki/Template:Bioinformatics" title="Template:Bioinformatics"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Bioinformatics" title="Template talk:Bioinformatics"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Bioinformatics" title="Special:EditPage/Template:Bioinformatics"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Bioinformatics" style="font-size:114%;margin:0 4em"><a href="/wiki/Bioinformatics" title="Bioinformatics">Bioinformatics</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%">Databases</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Sequence databases: <a href="/wiki/GenBank" title="GenBank">GenBank</a>, <a href="/wiki/European_Nucleotide_Archive" title="European Nucleotide Archive">European Nucleotide Archive</a>, <a href="/wiki/DNA_Data_Bank_of_Japan" title="DNA Data Bank of Japan">DNA Data Bank of Japan</a> and <a href="/wiki/China_National_GeneBank" title="China National GeneBank">China National GeneBank</a></li> <li>Secondary databases: <a href="/wiki/UniProt" title="UniProt">UniProt</a>, database of protein sequences grouping together <a href="/wiki/UniProt#UniProtKB.2FSwiss-Prot" title="UniProt">Swiss-Prot</a>, <a href="/wiki/UniProt#UniProtKB.2FTrEMBL" title="UniProt">TrEMBL</a> and <a href="/wiki/Protein_Information_Resource" title="Protein Information Resource">Protein Information Resource</a></li> <li>Other databases: <a href="/wiki/BioNumbers" title="BioNumbers">BioNumbers</a>, <a href="/wiki/Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a>, <a href="/wiki/Ensembl_genome_database_project" title="Ensembl genome database project">Ensembl</a>, <a href="/wiki/InterPro" title="InterPro">InterPro</a>, <a href="/wiki/KEGG" title="KEGG">KEGG</a>, and <a href="/wiki/Gene_ontology" class="mw-redirect" title="Gene ontology">Gene Ontology</a></li> <li>Specialised genomic databases: <a href="/wiki/Barcode_of_Life_Data_System" title="Barcode of Life Data System">BOLD</a>, <a href="/wiki/Saccharomyces_Genome_Database" title="Saccharomyces Genome Database">Saccharomyces Genome Database</a>, <a href="/wiki/FlyBase" title="FlyBase">FlyBase</a>, <a href="/wiki/VectorBase" title="VectorBase">VectorBase</a>, <a href="/wiki/WormBase" title="WormBase">WormBase</a>, <a href="/wiki/Rat_Genome_Database" title="Rat Genome Database">Rat Genome Database</a>, <a href="/wiki/PHI-base" title="PHI-base">PHI-base</a>, <a href="/wiki/The_Arabidopsis_Information_Resource" title="The Arabidopsis Information Resource">Arabidopsis Information Resource</a>, <a href="/wiki/GISAID" title="GISAID">GISAID</a> and <a href="/wiki/Zebrafish_Information_Network" title="Zebrafish Information Network">Zebrafish Information Network</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Software</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a></li> <li><a href="/wiki/Bowtie_(sequence_analysis)" title="Bowtie (sequence analysis)">Bowtie</a></li> <li><a href="/wiki/Clustal" title="Clustal">Clustal</a></li> <li><a class="mw-selflink selflink">EMBOSS</a></li> <li><a href="/wiki/HMMER" title="HMMER">HMMER</a></li> <li><a href="/wiki/MUSCLE_(alignment_software)" title="MUSCLE (alignment software)">MUSCLE</a></li> <li><a href="/wiki/Phylogenetic_Assignment_of_Named_Global_Outbreak_Lineages" title="Phylogenetic Assignment of Named Global Outbreak Lineages">PANGOLIN</a></li> <li><a href="/wiki/SAMtools" title="SAMtools">SAMtools</a></li> <li><a href="/wiki/Short_Oligonucleotide_Analysis_Package" title="Short Oligonucleotide Analysis Package">SOAP suite</a></li> <li><a href="/wiki/TopHat_(bioinformatics)" title="TopHat (bioinformatics)">TopHat</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Other</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li>Server: <a href="/wiki/ExPASy" class="mw-redirect" title="ExPASy">ExPASy</a></li> <li><a href="/wiki/Rosalind_(education_platform)" title="Rosalind (education platform)">Rosalind (education platform)</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Institutions</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Broad_Institute" title="Broad Institute">Broad Institute</a></li> <li><a href="/wiki/Computational_Biology_Department" class="mw-redirect" title="Computational Biology Department">Computational Biology Department</a> (CBD)</li> <li><a href="/wiki/COSBI" title="COSBI">Microsoft Research - University of Trento Centre for Computational and Systems Biology</a> (COSBI)</li> <li><a href="/wiki/Database_Center_for_Life_Science" title="Database Center for Life Science">Database Center for Life Science</a> (DBCLS)</li> <li><a href="/wiki/DNA_Data_Bank_of_Japan" title="DNA Data Bank of Japan">DNA Data Bank of Japan</a> (DDBJ)</li> <li><a href="/wiki/European_Bioinformatics_Institute" title="European Bioinformatics Institute">European Bioinformatics Institute</a> (EMBL-EBI)</li> <li><a href="/wiki/European_Molecular_Biology_Laboratory" title="European Molecular Biology Laboratory">European Molecular Biology Laboratory</a> (EMBL)</li> <li><a href="/wiki/Flatiron_Institute" title="Flatiron Institute">Flatiron Institute</a></li> <li><a href="/wiki/J._Craig_Venter_Institute" title="J. Craig Venter Institute">J. Craig Venter Institute</a> (JCVI)</li> <li><a href="/wiki/Max_Planck_Institute_of_Molecular_Cell_Biology_and_Genetics" title="Max Planck Institute of Molecular Cell Biology and Genetics">Max Planck Institute of Molecular Cell Biology and Genetics</a> (MPI-CBG)</li> <li><a href="/wiki/National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">US National Center for Biotechnology Information</a> (NCBI)</li> <li><a href="/wiki/National_Institute_of_Genetics" title="National Institute of Genetics">Japanese Institute of Genetics</a></li> <li><a href="/wiki/Netherlands_Bioinformatics_Centre" title="Netherlands Bioinformatics Centre">Netherlands Bioinformatics Centre</a> (NBIC)</li> <li><a href="/wiki/Philippine_Genome_Center" title="Philippine Genome Center">Philippine Genome Center</a> (PGC)</li> <li><a href="/wiki/Scripps_Research" title="Scripps Research">Scripps Research</a></li> <li><a href="/wiki/Swiss_Institute_of_Bioinformatics" title="Swiss Institute of Bioinformatics">Swiss Institute of Bioinformatics</a> (SIB)</li> <li><a href="/wiki/Wellcome_Sanger_Institute" title="Wellcome Sanger Institute">Wellcome Sanger Institute</a></li> <li><a href="/wiki/Whitehead_Institute" title="Whitehead Institute">Whitehead Institute</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Organizations</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/African_Society_for_Bioinformatics_and_Computational_Biology" title="African Society for Bioinformatics and Computational Biology">African Society for Bioinformatics and Computational Biology</a> (ASBCB)</li> <li><a href="/wiki/Australia_Bioinformatics_Resource" title="Australia Bioinformatics Resource">Australia Bioinformatics Resource</a> (EMBL-AR)</li> <li><a href="/wiki/EMBnet" title="EMBnet">European Molecular Biology network</a> (EMBnet)</li> <li><a href="/wiki/International_Nucleotide_Sequence_Database_Collaboration" title="International Nucleotide Sequence Database Collaboration">International Nucleotide Sequence Database Collaboration</a> (INSDC)</li> <li><a href="/wiki/International_Society_for_Biocuration" title="International Society for Biocuration">International Society for Biocuration</a> (ISB)</li> <li><a href="/wiki/International_Society_for_Computational_Biology" title="International Society for Computational Biology">International Society for Computational Biology</a> (ISCB) <ul><li><a href="/wiki/International_Society_for_Computational_Biology_Student_Council" title="International Society for Computational Biology Student Council">Student Council</a> (ISCB-SC)</li></ul></li> <li><a href="/wiki/Institute_of_Genomics_and_Integrative_Biology" title="Institute of Genomics and Integrative Biology">Institute of Genomics and Integrative Biology</a> (CSIR-IGIB)</li> <li><a href="/wiki/Japanese_Society_for_Bioinformatics" title="Japanese Society for Bioinformatics">Japanese Society for Bioinformatics</a> (JSBi)</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Meetings</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Basel_Computational_Biology_Conference" title="Basel Computational Biology Conference">Basel Computational Biology Conference‎</a> ([BC<sup>2</sup>])</li> <li><a href="/wiki/European_Conference_on_Computational_Biology" title="European Conference on Computational Biology">European Conference on Computational Biology</a> (ECCB)</li> <li><a href="/wiki/Intelligent_Systems_for_Molecular_Biology" title="Intelligent Systems for Molecular Biology">Intelligent Systems for Molecular Biology</a> (ISMB)</li> <li><a href="/wiki/International_Conference_on_Bioinformatics" title="International Conference on Bioinformatics">International Conference on Bioinformatics</a> (InCoB)</li> <li><a href="/wiki/International_Conference_on_Computational_Intelligence_Methods_for_Bioinformatics_and_Biostatistics" title="International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics">International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics</a> (CIBB)</li> <li><a href="/wiki/ISCB_Africa_ASBCB_Conference_on_Bioinformatics" title="ISCB Africa ASBCB Conference on Bioinformatics">ISCB Africa ASBCB Conference on Bioinformatics</a></li> <li><a href="/wiki/Pacific_Symposium_on_Biocomputing" title="Pacific Symposium on Biocomputing">Pacific Symposium on Biocomputing</a> (PSB)</li> <li><a href="/wiki/Research_in_Computational_Molecular_Biology" title="Research in Computational Molecular Biology">Research in Computational Molecular Biology</a> (RECOMB)</li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">File formats</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/CRAM_(file_format)" title="CRAM (file format)">CRAM format</a></li> <li><a href="/wiki/FASTA_format" title="FASTA format">FASTA format</a></li> <li><a href="/wiki/FASTQ_format" title="FASTQ format">FASTQ format</a></li> <li><a href="/wiki/NeXML_format" title="NeXML format">NeXML format</a></li> <li><a href="/wiki/Nexus_file" title="Nexus file">Nexus format</a></li> <li><a href="/wiki/Pileup_format" title="Pileup format">Pileup format</a></li> <li><a href="/wiki/SAM_(file_format)" title="SAM (file format)">SAM format</a></li> <li><a href="/wiki/Stockholm_format" title="Stockholm format">Stockholm format</a></li> <li><a href="/wiki/Variant_Call_Format" title="Variant Call Format">VCF format</a></li> <li><a href="/wiki/General_feature_format" title="General feature format">GFF format</a></li> <li><a href="/wiki/Gene_transfer_format" title="Gene transfer format">GTF format</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Related topics</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Computational_biology" title="Computational biology">Computational biology</a></li> <li><a href="/wiki/List_of_biobanks" title="List of biobanks">List of biobanks</a></li> <li><a href="/wiki/List_of_biological_databases" title="List of biological databases">List of biological databases</a></li> <li><a href="/wiki/Molecular_phylogenetics" title="Molecular phylogenetics">Molecular phylogenetics</a></li> <li><a href="/wiki/Sequencing" title="Sequencing">Sequencing</a></li> <li><a href="/wiki/Sequence_database" title="Sequence database">Sequence database</a></li> <li><a href="/wiki/Sequence_alignment" title="Sequence alignment">Sequence alignment</a></li></ul> </div></td></tr><tr><td class="navbox-abovebelow hlist" colspan="2"><div> <ul><li><span 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