NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

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

DESCRIPTION

       Find local sequence alignments.

       Score options (default settings): -r: match score   (DNA: 1, protein: blosum62, 0<Q<5:  6)
       -q: mismatch cost (DNA: 1, protein: blosum62, 0<Q<5: 18) -p: file for residue pair  scores
       -a:  gap  existence  cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost (DNA: 1,
       protein:  2, 0<Q<5:  9) -A: insertion existence cost (a) -B: insertion extension cost  (b)
       -c:  unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score drop
       for gapped alignments (max[y, e-1]) -y: maximum score drop for gapless  alignments  (t*10)
       -z:  maximum  score  drop  for  final  gapped alignments (x) -d: minimum score for gapless
       alignments (min[e, t*ln(1000*refSize/n)]) -e: minimum score for  gapped  alignments  (DNA:
       40, protein: 100, 0<Q<5: 180)

       Cosmetic  options  (default settings): -h: show all options and their default settings -v:
       be verbose: write messages about what lastal is doing -o: output file -f:  output  format:
       0=tabular, 1=maf (1)

       Miscellaneous  options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for
       DNA, 1 for protein) -T: type of alignment: 0=local,  1=overlap  (0)  -m:  maximum  initial
       matches  per  query position (10) -l: length threshold for initial matches (1 if -j0, else
       infinity) -n: maximum gapless alignments per query position (infinity if m=0, else m)  -k:
       step-size  along  the  query  sequence  (1)  -i: query batch size (8 KiB, unless there are
       multiple lastdb volumes) -u: mask lowercase during extensions: 0=never, 1=gapless,

              2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)

       -w: supress repeats inside exact matches, offset by  this  distance  or  less  (1000)  -G:
       genetic  code  file -t: 'temperature' for calculating probabilities (1/lambda) -g: 'gamma'
       parameter for gamma-centroid and LAMA (1) -j:  output  type:  0=match  counts,  1=gapless,
       2=redundant gapped, 3=gapped,

              4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)

       -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

              4=prb, 5=PSSM (0)

REPORTING BUGS

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