Linked Life Data

14705025

Source:http://linkedlifedata.com/resource/pubmed/id/14705025

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2004-1-5
pubmed:abstractText
An algorithm was developed to locally optimize gaps from the FSSP database. Over 2 million gaps were identified from all versus all FSSP structure comparisons, and datasets of non-identical gaps and flanking regions comprising between 90,000 and 135,000 sequence fragments were extracted for statistical analysis. Relative to background frequencies, gaps were enriched in residue types with small side chains and high turn propensity (D, G, N, P, S), and were depleted in residue types with hydrophobic side chains (C, F, I, L, V, W, Y). In contrast, regions flanking a gap exhibited opposite trends in amino acid frequencies, i.e., enrichment in hydrophobic residues and a high degree of secondary structure. Log-odds scores of residue type as a function of position in or around a gap were derived from the statistics. Three simple experiments demonstrated that these scores contained significant predictive information. First, regions where gaps were observed in single sequences taken from HOMSTRAD structure-based multiple sequence alignments generally scored higher than regions where gaps were not observed. Second, given the correct pairwise-aligned cores, the actual positions of gaps could be reproduced from sequence more accurately using the structurally-derived statistics than by using random pairwise alignments. Finally, revision of the Clustal-W residue-specific gap opening parameters with this new information improved the agreement of Clustal-W alignments with the structure-based alignments. At least three applications for these results are envisioned: improvement of gap penalties in pairwise (or multiple) sequence alignment, prediction of regions of single sequences likely (or unlikely) to contain indels, and more accurate placement of gaps in automated pairwise structure alignment.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
1097-0134
pubmed:author
pubmed:copyrightInfo
Copyright 2003 Wiley-Liss, Inc.
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
54
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
71-87
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
pubmed:affiliation
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.
pubmed:publicationType
Journal Article, Evaluation Studies