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lastal

NAME

lastal - genome-scale comparison of biological sequences

SYNOPSIS

lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

Find local sequence alignments.

Main options (default settings): -h: show all options and their default settings -o: output file -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -f: output format: 0=tabular, 1=maf (1)

Score parameters (default settings): -r: match score (DNA: 1, protein: blosum62, Q>0: 6) -q: mismatch cost (DNA: 1, protein: blosum62, Q>0: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, Q>0: 21) -b: gap extension cost (DNA: 1, protein: 2, Q>0: 9) -c: unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score dropoff for gapped extensions (max[y, a+b*20]) -y: maximum score dropoff for gapless extensions (t*10) -d: minimum score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, Q>0: 180)

Miscellaneous options (default settings): -Q: input format: 0=FASTA, 1=FASTQ-Sanger, 2=FASTQ-Solexa, 3=PRB (0) -u: mask lowercase during extensions: 0=neither, 1=gapless, 2=gapless+gapped (0) -m: maximum multiplicity for initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k: step-size along the query sequence (1) -i: query batch size (16 MiB if j=0, else 1 MiB if Q>0, else 128 MiB) -w: supress repeats within this distance inside large exact matches (1000) -t: 'temperature' for calculating probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid alignment (1) -G: genetic code file -v: be verbose: write messages about what lastal is doing -j: output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,

4=probabilities, 5=centroid (3)

REPORTING BUGS

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