Linked Life Data

772222

Source:http://linkedlifedata.com/resource/pubmed/id/772222

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
1976-7-6
pubmed:abstractText
The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
0022-2844
pubmed:author
pubmed:issnType
Print
pubmed:day
29
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
133-49
pubmed:dateRevised
2010-11-18
pubmed:meshHeading
pubmed:year
1976
pubmed:articleTitle
Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA.
pubmed:publicationType
Journal Article