Linked Life Data

18428783

Source:http://linkedlifedata.com/resource/pubmed/id/18428783

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PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2008-4-22
pubmed:abstractText
The PHRAP assembly program provides rapid comparison, alignment, and assembly of large sets of DNA sequences. PHRAP compares sequences by searching for pairs of perfectly matching "words" or sequence regions that meet certain criteria. If a match is found, PHRAP then tries to extend the alignment into overlapping sections called contigs. PHRAP uses quality values produced by the PHRED basecaller to strike a balance between tolerance of discrepancies and prevention of stacking repeat sequences. The PHRAP assembly algorithm is generally used as part of the PHRED/PHRAP/Consed software suite for sequence analysis. This unit presents instructions for basic usage of the PHRAP assembler, including preparation of the input files (Support Protocols 1 and 2) and explanation of output files (Basic Protocols 1 and 2). Several command line options for changing the PHRAP assembly parameters are also discussed (Basic Protocol 3).
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1934-340X
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
Chapter 11
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
Unit11.4
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Assembling genomic DNA sequences with PHRAP.
pubmed:affiliation
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
pubmed:publicationType
Journal Article