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/