Distribution of indel lengths
dc.contributor.author | Qian, Bin | en_US |
dc.contributor.author | Goldstein, Richard A. | en_US |
dc.date.accessioned | 2006-04-19T14:01:58Z | |
dc.date.available | 2006-04-19T14:01:58Z | |
dc.date.issued | 2001-10-01 | en_US |
dc.identifier.citation | Qian, 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.issn | 0887-3585 | en_US |
dc.identifier.issn | 1097-0134 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/34973 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=11536366&dopt=citation | en_US |
dc.description.abstract | Protein 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.extent | 84870 bytes | |
dc.format.extent | 3118 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
dc.language.iso | en_US | |
dc.publisher | John Wiley & Sons, Inc. | en_US |
dc.subject.other | Chemistry | en_US |
dc.subject.other | Biochemistry and Biotechnology | en_US |
dc.title | Distribution of indel lengths | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Molecular, Cellular and Developmental Biology | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Biophysics Research Division, University of Michigan, Ann Arbor, Michigan | en_US |
dc.contributor.affiliationum | Biophysics 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 48109-1055 | en_US |
dc.identifier.pmid | 11536366 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/34973/1/1129_ftp.pdf | en_US |
dc.identifier.doi | http://dx.doi.org/10.1002/prot.1129 | en_US |
dc.identifier.source | Proteins: Structure, Function, and Genetics | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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