:: DESCRIPTION
find_max_cover (FindMaxCover) finds the combination of local alignments that covers the maximum number of residues in a query sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Conant, G. C., and A. Wagner, (2004)
A fast algorithm for determining the best combination of local alignments to a query sequence,
BMC Bioinformatics, 5: 62.
:: DESCRIPTION
BLASR is a software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.
::DEVELOPER
Pacific Biosciences of California, Inc
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Sep 19;13:238. doi: 10.1186/1471-2105-13-238.
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.
Chaisson MJ, Tesler G.
:: DESCRIPTION
BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments , BWT-SW finds all local alignments1. The running speed of BWT-SW depends on the lengths of the database sequence and the query sequence. On a set of experiments using human genome as the database sequence, BWT-SW takes the same order of time as BLASTn on query sequences of length 1000 nucleotides or less . As far as we know, BWT-SW is the first practical tool that can find all local alignments.
::DEVELOPER
C.K. Wong (ckwong3@cs.hku.hk)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
T.W. Lam; W.K. Sung; S.L. Tam; C.K. Wong; S.M. Yiu.
Compressed Indexing and Local Alignment of DNA
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn032
