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