SANSparallel: interactive homology search against Uniprot
Identifieur interne : 000070 ( Pmc/Checkpoint ); précédent : 000069; suivant : 000071SANSparallel: interactive homology search against Uniprot
Auteurs : Panu Somervuo [Finlande] ; Liisa Holm [Finlande]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2015.
Abstract
Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at
Url:
DOI: 10.1093/nar/gkv317
PubMed: 25855811
PubMed Central: 4489265
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SANSparallel: interactive homology search against Uniprot</title><author><name sortKey="Somervuo, Panu" sort="Somervuo, Panu" uniqKey="Somervuo P" first="Panu" last="Somervuo">Panu Somervuo</name><affiliation wicri:level="4"><nlm:aff id="AFF1">Institute of Biotechnology, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Institute of Biotechnology, University of Helsinki, PO Box 65</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Department of Biosciences, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Helsinki, PO Box 65</wicri:regionArea><orgName 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wicri:level="4"><nlm:aff id="AFF1">Institute of Biotechnology, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Institute of Biotechnology, University of Helsinki, PO Box 65</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Department of Biosciences, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Helsinki, PO Box 65</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Holm, Liisa" sort="Holm, Liisa" uniqKey="Holm L" first="Liisa" last="Holm">Liisa Holm</name><affiliation wicri:level="4"><nlm:aff id="AFF1">Institute of Biotechnology, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Institute of Biotechnology, University of Helsinki, PO Box 65</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF2">Department of Biosciences, University of Helsinki, PO Box 65, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Helsinki, PO Box 65</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at <ext-link ext-link-type="uri" xlink:href="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi">http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi</ext-link>. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S.F. Altschul</name></author><author><name sortKey="Madden, T L" uniqKey="Madden T">T.L. Madden</name></author><author><name sortKey="Sch Ffer, A A" uniqKey="Sch Ffer A">A.A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25855811</article-id><article-id pub-id-type="pmc">4489265</article-id><article-id pub-id-type="doi">10.1093/nar/gkv317</article-id><article-categories><subj-group subj-group-type="heading"><subject>Web Server issue</subject></subj-group></article-categories><title-group><article-title>SANSparallel: interactive homology search against Uniprot</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Somervuo</surname><given-names>Panu</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Holm</surname><given-names>Liisa</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF2"><sup>2</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><aff id="AFF1"><label>1</label>Institute of Biotechnology, University of Helsinki, PO Box 65, Finland</aff><aff id="AFF2"><label>2</label>Department of Biosciences, University of Helsinki, PO Box 65, Finland</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>To whom correspondence should be addressed. Tel: +358 294 191 59115; Fax: +358 294 59366; Email: <email>liisa.holm@helsinki.fi</email></corresp></author-notes><pub-date pub-type="ppub"><day>01</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>08</day><month>4</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>08</day><month>4</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>43</volume><issue>Web Server issue</issue><fpage>W24</fpage><lpage>W29</lpage><history><date date-type="accepted"><day>28</day><month>3</month><year>2015</year></date><date date-type="rev-recd"><day>18</day><month>3</month><year>2015</year></date><date date-type="received"><day>05</day><month>2</month><year>2015</year></date></history><permissions><copyright-statement>© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:href="gkv317.pdf"></self-uri><abstract><p>Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at <ext-link ext-link-type="uri" xlink:href="http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi">http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi</ext-link>. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest.</p></abstract><counts><page-count count="6"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>1 July 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>Finlande</li></country><region><li>Uusimaa</li></region><settlement><li>Helsinki</li></settlement><orgName><li>Université d'Helsinki</li></orgName></list><tree><country name="Finlande"><region name="Uusimaa"><name sortKey="Somervuo, Panu" sort="Somervuo, Panu" uniqKey="Somervuo P" first="Panu" last="Somervuo">Panu Somervuo</name></region><name sortKey="Holm, Liisa" sort="Holm, Liisa" uniqKey="Holm L" first="Liisa" last="Holm">Liisa Holm</name><name sortKey="Holm, Liisa" sort="Holm, Liisa" uniqKey="Holm L" first="Liisa" last="Holm">Liisa Holm</name><name sortKey="Somervuo, Panu" sort="Somervuo, Panu" uniqKey="Somervuo P" first="Panu" last="Somervuo">Panu Somervuo</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= SANSparallel: interactive homology search against Uniprot
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Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:25855811" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |