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/