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/

lastal 393                                        January 2014                                         LASTAL(1)