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, 0<Q<5:  6) -q: mismatch cost
       (DNA: 1, 0<Q<5: 18) -p: match/mismatch score matrix (protein-protein:  BL62,  DNA-protein:
       BL80) -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 (off) -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

       E-value options (default settings): -D: query letters per  random  alignment  (1e+06)  -E:
       maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)

       Cosmetic  options  (default  settings):  -h,  --help:  show  all options and their default
       settings, and exit -V, --version: show version information, and exit -v: be verbose: write
       messages about what lastal is doing -f: output format: TAB, MAF, BlastTab (MAF)

       Miscellaneous  options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for
       DNA, 1 for protein) -S: score matrix applies to forward strand  of:  0=reference,  1=query
       (0)  -T:  type  of alignment: 0=local, 1=overlap (0) -m: maximum initial matches per query
       position (10) -l: minimum length for initial matches (1) -L: maximum  length  for  initial
       matches  (infinity)  -n:  maximum  gapless alignments per query position (infinity if m=0,
       else m) -C: omit gapless alignments in >= C others with > score-per-length (off) -K:  omit
       alignments  whose  query  range lies in >= K others with > score (off) -k: step-size along
       the query sequence (1) -i: query batch size (8 KiB, unless there is > 1 thread  or  lastdb
       volume)  -P:  number  of  parallel threads (1) -R: repeat-marking options (the same as was
       used for lastdb) -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: suppress repeats inside exact matches, offset by <= this distance (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, 7=expected counts (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/