Linked Life Data

14980022

Source:http://linkedlifedata.com/resource/pubmed/id/14980022

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
2004-2-24
pubmed:abstractText
Substitution matrices have been useful for sequence alignment and protein sequence comparisons. The BLOSUM series of matrices, which had been derived from a database of alignments of protein blocks, improved the accuracy of alignments previously obtained from the PAM-type matrices estimated from only closely related sequences. Although BLOSUM matrices are scoring matrices now widely used for protein sequence alignments, they do not describe an evolutionary model. BLOSUM matrices do not permit the estimation of the actual number of amino acid substitutions between sequences by correcting for multiple hits. The method presented here uses the Blocks database of protein alignments, along with the additivity of evolutionary distances, to approximate the amino acid substitution probabilities as a function of actual evolutionary distance. The PMB (Probability Matrix from Blocks) defines a new evolutionary model for protein evolution that can be used for evolutionary analyses of protein sequences. Our model is directly derived from, and thus compatible with, the BLOSUM matrices. The model has the additional advantage of being easily implemented.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1066-5277
pubmed:author
pubmed:issnType
Print
pubmed:volume
10
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
997-1010
pubmed:meshHeading
pubmed:year
2003
pubmed:articleTitle
A transition probability model for amino acid substitutions from blocks.
pubmed:affiliation
Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
pubmed:publicationType
Journal Article