CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences
Identifieur interne : 000586 ( Main/Exploration ); précédent : 000585; suivant : 000587CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences
Auteurs : Charalambos Chrysostomou [Royaume-Uni] ; Huseyin Seker [Royaume-Uni] ; Nizamettin Aydin [Turquie]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2015.
Abstract
Complex informational spectrum analysis for protein sequences (CISAPS) and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.
Url:
DOI: 10.1155/2015/909765
PubMed: 25632276
PubMed Central: 4302972
Affiliations:
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wicri:level="1"><nlm:aff id="I2">Department of Computer Science and Digital Technologies, Faculty of Engineering and Environment, The University of Northumbria at Newcastle, Newcastle-upon-Tyne NE1 8ST, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Computer Science and Digital Technologies, Faculty of Engineering and Environment, The University of Northumbria at Newcastle, Newcastle-upon-Tyne NE1 8ST</wicri:regionArea><wicri:noRegion>Newcastle-upon-Tyne NE1 8ST</wicri:noRegion></affiliation></author><author><name sortKey="Aydin, Nizamettin" sort="Aydin, Nizamettin" uniqKey="Aydin N" first="Nizamettin" last="Aydin">Nizamettin Aydin</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Engineering, Yildiz Technical University, 34220 Istanbul, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Computer Engineering, Yildiz Technical University, 34220 Istanbul</wicri:regionArea><wicri:noRegion>34220 Istanbul</wicri:noRegion></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</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>Complex informational spectrum analysis for protein sequences (CISAPS) and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.</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="Gish, W" uniqKey="Gish W">W. Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W. Miller</name></author><author><name sortKey="Myers, E W" uniqKey="Myers E">E. W. Myers</name></author><author><name sortKey="Lipman, D J" uniqKey="Lipman D">D. J. Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grassmann, J" uniqKey="Grassmann J">J. Grassmann</name></author><author><name sortKey="Reczko, M" uniqKey="Reczko M">M. Reczko</name></author><author><name sortKey="Suhai, S" uniqKey="Suhai S">S. Suhai</name></author><author><name sortKey="Edler, L" uniqKey="Edler L">L. 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Stewart</name></author><author><name sortKey="Maring, C J" uniqKey="Maring C">C. J. Maring</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fernandez, L" uniqKey="Fernandez L">L. Fernández</name></author><author><name sortKey="Caballero, J" uniqKey="Caballero J">J. Caballero</name></author><author><name sortKey="Abreu, J I" uniqKey="Abreu J">J. I. Abreu</name></author><author><name sortKey="Fernandez, M" uniqKey="Fernandez M">M. Fernández</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Norbert, N" uniqKey="Norbert N">N. Norbert</name></author><author><name sortKey="Seker, H" uniqKey="Seker H">H. Seker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, W" uniqKey="Hu W">W. 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