SANSparallel: interactive homology search against Uniprot
Identifieur interne : 000076 ( Main/Merge ); précédent : 000075; suivant : 000077SANSparallel: 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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000063
- to stream Pmc, to step Curation: 000063
- to stream Pmc, to step Checkpoint: 000070
- to stream Ncbi, to step Merge: 000618
- to stream Ncbi, to step Curation: 000618
- to stream Ncbi, to step Checkpoint: 000618
Links to Exploration step
PMC:4489265Le document en format XML
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<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>
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<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. Schäffer</name>
</author>
<author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name>
</author>
<author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z. Zhang</name>
</author>
<author><name sortKey="Miller, W" uniqKey="Miller W">W. Miller</name>
</author>
<author><name sortKey="Lipman, D J" uniqKey="Lipman D">D.J. Lipman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mcginnis, S" uniqKey="Mcginnis S">S. McGinnis</name>
</author>
<author><name sortKey="Madden, T L" uniqKey="Madden T">T.L. Madden</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Finn, R D" uniqKey="Finn R">R.D. Finn</name>
</author>
<author><name sortKey="Clements, J" uniqKey="Clements J">J. Clements</name>
</author>
<author><name sortKey="Eddy, S R" uniqKey="Eddy S">S.R. Eddy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name>
</author>
<author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name>
</author>
<author><name sortKey="Li, W" uniqKey="Li W">W. Li</name>
</author>
<author><name sortKey="Altinatas, I" uniqKey="Altinatas I">I. Altinatas</name>
</author>
<author><name sortKey="Lin, A" uniqKey="Lin A">A. Lin</name>
</author>
<author><name sortKey="Peltier, S" uniqKey="Peltier S">S. Peltier</name>
</author>
<author><name sortKey="Stocks, K" uniqKey="Stocks K">K. Stocks</name>
</author>
<author><name sortKey="Allen, E E" uniqKey="Allen E">E.E. Allen</name>
</author>
<author><name sortKey="Ellisman, M" uniqKey="Ellisman M">M. Ellisman</name>
</author>
<author><name sortKey="Grethe, J" uniqKey="Grethe J">J. Grethe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Heger, A" uniqKey="Heger A">A. Heger</name>
</author>
<author><name sortKey="Korpelainen, E" uniqKey="Korpelainen E">E. Korpelainen</name>
</author>
<author><name sortKey="Hupponen, T" uniqKey="Hupponen T">T. Hupponen</name>
</author>
<author><name sortKey="Mattila, K" uniqKey="Mattila K">K. Mattila</name>
</author>
<author><name sortKey="Ollikainen, V" uniqKey="Ollikainen V">V. Ollikainen</name>
</author>
<author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rattei, T" uniqKey="Rattei T">T. Rattei</name>
</author>
<author><name sortKey="Arnold, R" uniqKey="Arnold R">R. Arnold</name>
</author>
<author><name sortKey="Tischler, P" uniqKey="Tischler P">P. Tischler</name>
</author>
<author><name sortKey="Lindner, D" uniqKey="Lindner D">D. Lindner</name>
</author>
<author><name sortKey="Stumpflen, V" uniqKey="Stumpflen V">V. Stümpflen</name>
</author>
<author><name sortKey="Mewes, H W" uniqKey="Mewes H">H.W. Mewes</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Koskinen, P" uniqKey="Koskinen P">P. Koskinen</name>
</author>
<author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kent, W J" uniqKey="Kent W">W.J. Kent</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y. Zhao</name>
</author>
<author><name sortKey="Tang, H" uniqKey="Tang H">H. Tang</name>
</author>
<author><name sortKey="Ye, Y" uniqKey="Ye Y">Y. Ye</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hauswedell, H" uniqKey="Hauswedell H">H. Hauswedell</name>
</author>
<author><name sortKey="Singer, J" uniqKey="Singer J">J. Singer</name>
</author>
<author><name sortKey="Reinert, K" uniqKey="Reinert K">K. Reinert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kielbasa, S M" uniqKey="Kielbasa S">S.M. Kielbasa</name>
</author>
<author><name sortKey="Wan, R" uniqKey="Wan R">R. Wan</name>
</author>
<author><name sortKey="Sato, K" uniqKey="Sato K">K. Sato</name>
</author>
<author><name sortKey="Horton, P" uniqKey="Horton P">P. Horton</name>
</author>
<author><name sortKey="Frith, M C" uniqKey="Frith M">M.C. Frith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edgar, Robert C" uniqKey="Edgar R">Robert C. Edgar</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Buchfink, B" uniqKey="Buchfink B">B. Buchfink</name>
</author>
<author><name sortKey="Xie, C" uniqKey="Xie C">C. Xie</name>
</author>
<author><name sortKey="Huson, D H" uniqKey="Huson D">D.H. Huson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roytberg, M" uniqKey="Roytberg M">M. Roytberg</name>
</author>
<author><name sortKey="Gambin, A" uniqKey="Gambin A">A. Gambin</name>
</author>
<author><name sortKey="Noe, L" uniqKey="Noe L">L. Noé</name>
</author>
<author><name sortKey="Lasota, S" uniqKey="Lasota S">S. Lasota</name>
</author>
<author><name sortKey="Furletova, E" uniqKey="Furletova E">E. Furletova</name>
</author>
<author><name sortKey="Szczurek, E" uniqKey="Szczurek E">E. Szczurek</name>
</author>
<author><name sortKey="Kucherov, G" uniqKey="Kucherov G">G. Kucherov</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pearson, W R" uniqKey="Pearson W">W.R. Pearson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brown, N P" uniqKey="Brown N">N.P. Brown</name>
</author>
<author><name sortKey="Leroy, C" uniqKey="Leroy C">C. Leroy</name>
</author>
<author><name sortKey="Sander, C" uniqKey="Sander C">C. Sander</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wheeler, T J" uniqKey="Wheeler T">T.J. Wheeler</name>
</author>
<author><name sortKey="Clements, J" uniqKey="Clements J">J. Clements</name>
</author>
<author><name sortKey="Finn, R D" uniqKey="Finn R">R.D. Finn</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Waterhouse, A M" uniqKey="Waterhouse A">A.M. Waterhouse</name>
</author>
<author><name sortKey="Procter, J B" uniqKey="Procter J">J.B. Procter</name>
</author>
<author><name sortKey="Martin, D M" uniqKey="Martin D">D.M. Martin</name>
</author>
<author><name sortKey="Clamp, M" uniqKey="Clamp M">M. Clamp</name>
</author>
<author><name sortKey="Barton, G J" uniqKey="Barton G">G.J. Barton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Korf, I" uniqKey="Korf I">I. Korf</name>
</author>
<author><name sortKey="Yandell, M" uniqKey="Yandell M">M. Yandell</name>
</author>
<author><name sortKey="Bedell, J" uniqKey="Bedell J">J. Bedell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name>
</author>
<author><name sortKey="Rosenstrom, P" uniqKey="Rosenstrom P">P. Rosenström</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Garlant, L" uniqKey="Garlant L">L. Garlant</name>
</author>
<author><name sortKey="Koskinen, P" uniqKey="Koskinen P">P. Koskinen</name>
</author>
<author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. Liu</name>
</author>
<author><name sortKey="Nykyri, J" uniqKey="Nykyri J">J. Nykyri</name>
</author>
<author><name sortKey="Ahamed, S" uniqKey="Ahamed S">S. Ahamed</name>
</author>
<author><name sortKey="Rouhiainen, L" uniqKey="Rouhiainen L">L. Rouhiainen</name>
</author>
<author><name sortKey="Laine, P" uniqKey="Laine P">P. Laine</name>
</author>
<author><name sortKey="Paulin, L" uniqKey="Paulin L">L. Paulin</name>
</author>
<author><name sortKey="Auvinen, P" uniqKey="Auvinen P">P. Auvinen</name>
</author>
<author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ahola, V" uniqKey="Ahola V">V. Ahola</name>
</author>
<author><name sortKey="Lehtonen, R" uniqKey="Lehtonen R">R. Lehtonen</name>
</author>
<author><name sortKey="Somervuo, P" uniqKey="Somervuo P">P. Somervuo</name>
</author>
<author><name sortKey="Salmela, L" uniqKey="Salmela L">L. Salmela</name>
</author>
<author><name sortKey="Koskinen, P" uniqKey="Koskinen P">P. Koskinen</name>
</author>
<author><name sortKey="Rastas, P" uniqKey="Rastas P">P. Rastas</name>
</author>
<author><name sortKey="V Lim Ki, N" uniqKey="V Lim Ki N">N. Välimäki</name>
</author>
<author><name sortKey="Paulin, L" uniqKey="Paulin L">L. Paulin</name>
</author>
<author><name sortKey="Kvist, J" uniqKey="Kvist J">J. Kvist</name>
</author>
<author><name sortKey="Wahlberg, N" uniqKey="Wahlberg N">N. Wahlberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Koskinen, P" uniqKey="Koskinen P">P. Koskinen</name>
</author>
<author><name sortKey="Toronen, P" uniqKey="Toronen P">P. Toronen</name>
</author>
<author><name sortKey="Nokso Koivisto, J" uniqKey="Nokso Koivisto J">J. Nokso-Koivisto</name>
</author>
<author><name sortKey="Holm, L" uniqKey="Holm L">L. Holm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="O Donoghue, S I" uniqKey="O Donoghue S">S.I. O'Donoghue</name>
</author>
<author><name sortKey="Sabir, K S" uniqKey="Sabir K">K.S. Sabir</name>
</author>
<author><name sortKey="Kalemanov, M" uniqKey="Kalemanov M">M. Kalemanov</name>
</author>
<author><name sortKey="Stolte, C" uniqKey="Stolte C">C. Stolte</name>
</author>
<author><name sortKey="Wellmann, B" uniqKey="Wellmann B">B. Wellmann</name>
</author>
<author><name sortKey="Ho, V" uniqKey="Ho V">V. Ho</name>
</author>
<author><name sortKey="Roos, M" uniqKey="Roos M">M. Roos</name>
</author>
<author><name sortKey="Perdigao, N" uniqKey="Perdigao N">N. Perdigão</name>
</author>
<author><name sortKey="Buske, F A" uniqKey="Buske F">F.A. Buske</name>
</author>
<author><name sortKey="Heinrich, J" uniqKey="Heinrich J">J. Heinrich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rost, B" uniqKey="Rost B">B. Rost</name>
</author>
<author><name sortKey="Sander, C" uniqKey="Sander C">C. Sander</name>
</author>
</analytic>
</biblStruct>
</listBibl>
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