SYNOPSIS

lastal [,options/] ,lastdb-name fasta-sequence-file(s)/

DESCRIPTION

Find local sequence alignments.

Score options (default settings): -r: match score (2 if -M, else 6 if 0<Q<5, else 1 if DNA) -q: mismatch cost (3 if -M, else 18 if 0<Q<5, else 1 if DNA) -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, BlastTab+ (MAF)

Initial-match options (default settings): -m: maximum initial matches per query position (10) -l: minimum length for initial matches (1) -L: maximum length for initial matches (infinity) -k: use initial matches starting at every k-th position in each query (1) -W: use "minimum" positions in sliding windows of W consecutive positions

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) -M: find minimum-difference alignments (faster but cruder) -T: type of alignment: 0=local, 1=overlap (0) -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) -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+postmask, 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/