Linked Life Data

1774068

Source:http://linkedlifedata.com/resource/pubmed/id/1774068

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
1992-3-5
pubmed:abstractText
The sensitivity and selectivity of the FASTA and the Smith-Waterman protein sequence comparison algorithms were evaluated using the superfamily classification provided in the National Biomedical Research Foundation/Protein Identification Resource (PIR) protein sequence database. Sequences from each of the 34 superfamilies in the PIR database with 20 or more members were compared against the protein sequence database. The similarity scores of the related and unrelated sequences were determined using either the FASTA program or the Smith-Waterman local similarity algorithm. These two sets of similarity scores were used to evaluate the ability of the two comparison algorithms to identify distantly related protein sequences. The FASTA program using the ktup = 2 sensitivity setting performed as well as the Smith-Waterman algorithm for 19 of the 34 superfamilies. Increasing the sensitivity by setting ktup = 1 allowed FASTA to perform as well as Smith-Waterman on an additional 7 superfamilies. The rigorous Smith-Waterman method performed better than FASTA with ktup = 1 on 8 superfamilies, including the globins, immunoglobulin variable regions, calmodulins, and plastocyanins. Several strategies for improving the sensitivity of FASTA were examined. The greatest improvement in sensitivity was achieved by optimizing a band around the best initial region found for every library sequence. For every superfamily except the globins and immunoglobulin variable regions, this strategy was as sensitive as a full Smith-Waterman. For some sequences, additional sensitivity was achieved by including conserved but nonidentical residues in the lookup table used to identify the initial region.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Nov
pubmed:issn
0888-7543
pubmed:author
pubmed:issnType
Print
pubmed:volume
11
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
635-50
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
1991
pubmed:articleTitle
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
pubmed:affiliation
Department of Biochemistry, University of Virginia, Charlottesville 22908.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S.