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Distribution of indel lengths

dc.contributor.authorQian, Binen_US
dc.contributor.authorGoldstein, Richard A.en_US
dc.date.accessioned2006-04-19T14:01:58Z
dc.date.available2006-04-19T14:01:58Z
dc.date.issued2001-10-01en_US
dc.identifier.citationQian, Bin; Goldstein, Richard A. (2001)."Distribution of indel lengths." Proteins: Structure, Function, and Genetics 45(1): 102-104. <http://hdl.handle.net/2027.42/34973>en_US
dc.identifier.issn0887-3585en_US
dc.identifier.issn1097-0134en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/34973
dc.identifier.urihttp://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=11536366&dopt=citationen_US
dc.description.abstractProtein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with initializing a gap, it is still an obvious oversimplification of the real processes that occur during sequence evolution. To improve the efficiency of sequence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertions and deletions in homologous proteins. In this work, we extract the probability of a gap occurrence and the resulting gap length distribution in distantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fitted with a multiexponential with four distinct components. The results suggest new approaches to modeling insertions and deletions in sequence alignments. Proteins 2001;45:102–104. © 2001 Wiley-Liss, Inc.en_US
dc.format.extent84870 bytes
dc.format.extent3118 bytes
dc.format.mimetypeapplication/pdf
dc.format.mimetypetext/plain
dc.language.isoen_US
dc.publisherJohn Wiley & Sons, Inc.en_US
dc.subject.otherChemistryen_US
dc.subject.otherBiochemistry and Biotechnologyen_US
dc.titleDistribution of indel lengthsen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biologyen_US
dc.subject.hlbtoplevelHealth Sciencesen_US
dc.description.peerreviewedPeer Revieweden_US
dc.contributor.affiliationumBiophysics Research Division, University of Michigan, Ann Arbor, Michiganen_US
dc.contributor.affiliationumBiophysics Research Division, University of Michigan, Ann Arbor, Michigan ; Department of Chemistry, University of Michigan, Ann Arbor, Michigan ; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055en_US
dc.identifier.pmid11536366en_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/34973/1/1129_ftp.pdfen_US
dc.identifier.doihttp://dx.doi.org/10.1002/prot.1129en_US
dc.identifier.sourceProteins: Structure, Function, and Geneticsen_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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