NAME¶

lastex - Calculate expected numbers of alignments for random sequences.

DESCRIPTION¶

Usage: lastex [options] reference-counts-file query-counts-file [alignments-file] Calculate expected numbers of alignments for random sequences. Options (default settings): -h: show all options and their default settings -s: strands (2 for DNA, 1 for protein) -r: match score (DNA: 1, protein: blosum62) -q: mismatch cost (DNA: 1, protein: blosum62) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11) -b: gap extension cost (DNA: 1, protein: 2) -g: do calculations for gapless alignments -y: find the expected number of alignments with score >= this -E: maximum expected number of alignments -z: calculate the expected number of alignments per:

0 = reference counts file / query counts file 1 = reference counts file / each query sequence 2 = each reference sequence / query counts file 3 = each reference sequence / each query sequence (0)

REPORTING BUGS¶

Report bugs to: last (ATmark) cbrc (dot) jp LAST home page: http://last.cbrc.jp/