Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio
Identifieur interne : 000C39 ( Main/Exploration ); précédent : 000C38; suivant : 000C40Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio
Auteurs : Klas Hatje [Allemagne] ; Oliver Keller [Allemagne] ; Björn Hammesfahr [Allemagne] ; Holger Pillmann [Allemagne] ; Stephan Waack [Allemagne] ; Martin Kollmar [Allemagne]Source :
- BMC Research Notes [ 1756-0500 ] ; 2011.
Abstract
Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons.
Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools.
With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio outperforms all other software tested. WebScipio has been restructured and provides easy access to the genome assemblies of about 640 eukaryotic species. Scipio and WebScipio are freely accessible at
Url:
DOI: 10.1186/1756-0500-4-265
PubMed: 21798037
PubMed Central: 3162530
Affiliations:
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Le document en format XML
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type="city">Göttingen</settlement></placeName></affiliation></author><author><name sortKey="Keller, Oliver" sort="Keller, Oliver" uniqKey="Keller O" first="Oliver" last="Keller">Oliver Keller</name><affiliation wicri:level="3"><nlm:aff id="I2">Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, 37077 Göttingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, 37077 Göttingen</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Göttingen</settlement></placeName></affiliation></author><author><name sortKey="Hammesfahr, Bjorn" sort="Hammesfahr, Bjorn" uniqKey="Hammesfahr B" first="Björn" last="Hammesfahr">Björn Hammesfahr</name><affiliation wicri:level="3"><nlm:aff id="I1">Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Göttingen</settlement></placeName></affiliation></author><author><name sortKey="Pillmann, Holger" sort="Pillmann, Holger" uniqKey="Pillmann H" first="Holger" last="Pillmann">Holger Pillmann</name><affiliation wicri:level="3"><nlm:aff id="I1">Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Göttingen</settlement></placeName></affiliation></author><author><name sortKey="Waack, Stephan" sort="Waack, Stephan" uniqKey="Waack S" first="Stephan" last="Waack">Stephan Waack</name><affiliation wicri:level="3"><nlm:aff id="I2">Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, 37077 Göttingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, 37077 Göttingen</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Göttingen</settlement></placeName></affiliation></author><author><name sortKey="Kollmar, Martin" sort="Kollmar, Martin" uniqKey="Kollmar M" first="Martin" last="Kollmar">Martin Kollmar</name><affiliation wicri:level="3"><nlm:aff id="I1">Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen</wicri:regionArea><placeName><region type="land" nuts="2">Basse-Saxe</region><settlement type="city">Göttingen</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Research Notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons.</p></sec><sec><title>Results</title><p>Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools.</p></sec><sec><title>Conclusions</title><p>With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio outperforms all other software tested. WebScipio has been restructured and provides easy access to the genome assemblies of about 640 eukaryotic species. Scipio and WebScipio are freely accessible at <ext-link ext-link-type="uri" xlink:href="http://www.webscipio.org">http://www.webscipio.org</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Mardis, Er" uniqKey="Mardis E">ER Mardis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardner, Mj" uniqKey="Gardner M">MJ Gardner</name></author><author><name sortKey="Hall, N" uniqKey="Hall N">N Hall</name></author><author><name sortKey="Fung, E" uniqKey="Fung E">E Fung</name></author><author><name sortKey="White, O" uniqKey="White O">O White</name></author><author><name sortKey="Berriman, M" uniqKey="Berriman M">M Berriman</name></author><author><name sortKey="Hyman, Rw" uniqKey="Hyman R">RW Hyman</name></author><author><name sortKey="Carlton, Jm" uniqKey="Carlton J">JM Carlton</name></author><author><name sortKey="Pain, A" uniqKey="Pain A">A Pain</name></author><author><name 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sortKey="Kucherlapati, R" uniqKey="Kucherlapati R">R Kucherlapati</name></author><author><name sortKey="Leinwand, L" uniqKey="Leinwand L">L Leinwand</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deutsch, M" uniqKey="Deutsch M">M Deutsch</name></author><author><name sortKey="Long, M" uniqKey="Long M">M Long</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benton, Mj" uniqKey="Benton M">MJ Benton</name></author><author><name sortKey="Donoghue, Pc" uniqKey="Donoghue P">PC Donoghue</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sayers, Ew" uniqKey="Sayers E">EW Sayers</name></author><author><name sortKey="Barrett, T" uniqKey="Barrett T">T Barrett</name></author><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author><author><name sortKey="Bolton, E" uniqKey="Bolton E">E Bolton</name></author><author><name sortKey="Bryant, Sh" uniqKey="Bryant S">SH Bryant</name></author><author><name sortKey="Canese, K" uniqKey="Canese K">K Canese</name></author><author><name sortKey="Chetvernin, V" uniqKey="Chetvernin V">V Chetvernin</name></author><author><name sortKey="Church, Dm" uniqKey="Church D">DM Church</name></author><author><name sortKey="Dicuccio, M" uniqKey="Dicuccio M">M DiCuccio</name></author><author><name sortKey="Federhen, S" uniqKey="Federhen S">S Federhen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Slater, Gs" uniqKey="Slater G">GS Slater</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Solovyev, V" uniqKey="Solovyev V">V Solovyev</name></author><author><name sortKey="Kosarev, P" uniqKey="Kosarev P">P Kosarev</name></author><author><name sortKey="Seledsov, I" uniqKey="Seledsov I">I Seledsov</name></author><author><name sortKey="Vorobyev, D" uniqKey="Vorobyev D">D Vorobyev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salamov, Aa" uniqKey="Salamov A">AA Salamov</name></author><author><name sortKey="Solovyev, Vv" uniqKey="Solovyev V">VV Solovyev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Clamp, M" uniqKey="Clamp M">M Clamp</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yeh, Rf" uniqKey="Yeh R">RF Yeh</name></author><author><name sortKey="Lim, Lp" uniqKey="Lim L">LP Lim</name></author><author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stanke, M" uniqKey="Stanke M">M Stanke</name></author><author><name sortKey="Waack, S" uniqKey="Waack S">S Waack</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name></author><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author><author><name sortKey="Schaffer, Aa" uniqKey="Schaffer A">AA Schaffer</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, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Basse-Saxe</li></region><settlement><li>Göttingen</li></settlement></list><tree><country name="Allemagne"><region name="Basse-Saxe"><name sortKey="Hatje, Klas" sort="Hatje, Klas" uniqKey="Hatje K" first="Klas" last="Hatje">Klas Hatje</name></region><name sortKey="Hammesfahr, Bjorn" sort="Hammesfahr, Bjorn" uniqKey="Hammesfahr B" first="Björn" last="Hammesfahr">Björn Hammesfahr</name><name sortKey="Keller, Oliver" sort="Keller, Oliver" uniqKey="Keller O" first="Oliver" last="Keller">Oliver Keller</name><name sortKey="Kollmar, Martin" sort="Kollmar, Martin" uniqKey="Kollmar M" first="Martin" last="Kollmar">Martin Kollmar</name><name sortKey="Pillmann, Holger" sort="Pillmann, Holger" uniqKey="Pillmann H" first="Holger" last="Pillmann">Holger Pillmann</name><name sortKey="Waack, Stephan" sort="Waack, Stephan" uniqKey="Waack S" first="Stephan" last="Waack">Stephan Waack</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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