Linked Life Data

21551146

Source:http://linkedlifedata.com/resource/pubmed/id/21551146

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
13
pubmed:dateCreated
2011-6-20
pubmed:abstractText
The large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses. AVAILABILITY: Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from http://sourceforge.net/projects/kmer/. CONTACT: florea@umiacs.umd.edu
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
1367-4811
pubmed:author
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
27
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1869-70
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.
pubmed:affiliation
The J. Craig Venter Institute, Rockville, MD 20850, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural