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Special Forums News, Links, Events and Announcements Software Releases - RSS News Basic Local Alignment Search Tool 2.2.19 (Default branch)
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Old 12-18-2008
Basic Local Alignment Search Tool 2.2.19 (Default branch)
BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems. License: Open Software License Changes:
The BLASTDB environment variable now supports multiple database search paths. When possible, a smaller protein lookup table is used to improve performance. formatrpsdb now supports creating databases larger than 2G. seedtop now supports searches with gi lists. The X3 value for blastn/megablast was corrected. Image

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LEARN ABOUT DEBIAN

lastal

LASTAL(1)							   User Commands							 LASTAL(1)

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,  pro-
       tein:   2,  0<Q<5:   9)	-c:  unaligned	residue  pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
       (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments  (x)  -d:  minimum
       score for gapless alignments (e*3/5) -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) -m: maximum multiplicity  for
       initial	matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
       step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128	MiB)  -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 (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastal 199							     May 2012								 LASTAL(1)