de la Bastide, M., McCombie, W. R. (March 2007) Assembling genomic DNA sequences with PHRAP. Current Protocols in Bioinformatics (Unit 1). ISSN 1934-340X (Electronic)1934-3396 (Linking)
Abstract
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).
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > annotation > sequence annotation bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering bioinformatics > genomics and proteomics > computers > computer software bioinformatics > genomics and proteomics > databases > databases |
| CSHL Authors: | |
| Communities: | CSHL labs > McCombie lab |
| Depositing User: | CSHL Librarian |
| Date: | March 2007 |
| Date Deposited: | 30 Nov 2011 19:40 |
| Last Modified: | 11 Apr 2013 19:41 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/22993 |
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