Genome-scale comparison of biological sequences
lastal [\,options\/] \,lastdb-name fasta-sequence-file(s)\/
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 (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 -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) -C: culling limit for gapless alignments (off) -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)
Report bugs to: last-align (ATmark) googlegroups (dot) com
LAST home page: http://last.cbrc.jp/