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Article: NdPASA: A pairwise sequence alignment server for distantly related proteins

TitleNdPASA: A pairwise sequence alignment server for distantly related proteins
Authors
Li, WWang, JFeng, JA
Issue Date2005
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2005, v. 21 n. 19, p. 3803-3805 How to Cite?
DOI: http://dx.doi.org/10.1093/bioinformatics/bti619
AbstractSummary: NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in the query sequence matching against a corresponding residue pair adopting a particular secondary structure in the template sequence. NdPASA is most effective in aligning homologous proteins sharing low percentage of sequence identity. The server is designed to aid homologous protein structure modeling. A PSI-BLAST search engine was implemented to help users identify template candidates that are most appropriate for modeling the query sequences. © The Author 2005. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/147527
ISSN
1367-4803
2023 Impact Factor: 4.4
2023 SCImago Journal Rankings: 2.574
ISI Accession Number ID
WOS:000232596100017
References
References in Scopus

 

DC FieldValueLanguage
dc.contributor.authorLi, Wen_US
dc.contributor.authorWang, Jen_US
dc.contributor.authorFeng, JAen_US
dc.date.accessioned2012-05-29T06:04:22Z-
dc.date.available2012-05-29T06:04:22Z-
dc.date.issued2005en_US
dc.identifier.citationBioinformatics, 2005, v. 21 n. 19, p. 3803-3805en_US
dc.identifier.issn1367-4803en_US
dc.identifier.urihttp://hdl.handle.net/10722/147527-
dc.description.abstractSummary: NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in the query sequence matching against a corresponding residue pair adopting a particular secondary structure in the template sequence. NdPASA is most effective in aligning homologous proteins sharing low percentage of sequence identity. The server is designed to aid homologous protein structure modeling. A PSI-BLAST search engine was implemented to help users identify template candidates that are most appropriate for modeling the query sequences. © The Author 2005. Published by Oxford University Press. All rights reserved.en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_US
dc.relation.ispartofBioinformaticsen_US
dc.subject.meshAlgorithmsen_US
dc.subject.meshAmino Acid Sequenceen_US
dc.subject.meshInterneten_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshProteins - Analysis - Chemistryen_US
dc.subject.meshSequence Alignment - Methodsen_US
dc.subject.meshSequence Analysis, Protein - Methodsen_US
dc.subject.meshSequence Homology, Amino Aciden_US
dc.subject.meshSoftwareen_US
dc.titleNdPASA: A pairwise sequence alignment server for distantly related proteinsen_US
dc.typeArticleen_US
dc.identifier.emailWang, J:junwen@hkucc.hku.hken_US
dc.identifier.authorityWang, J=rp00280en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1093/bioinformatics/bti619en_US
dc.identifier.pmid16105904-
dc.identifier.scopuseid_2-s2.0-27544439431en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-27544439431&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume21en_US
dc.identifier.issue19en_US
dc.identifier.spage3803en_US
dc.identifier.epage3805en_US
dc.identifier.isiWOS:000232596100017-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLi, W=36066858500en_US
dc.identifier.scopusauthoridWang, J=8950599500en_US
dc.identifier.scopusauthoridFeng, JA=7403884662en_US
dc.identifier.citeulike350692-
dc.identifier.issnl1367-4803-

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