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BLASTCL3(1)		   NCBI	Tools User's Manual		   BLASTCL3(1)

NAME
       blastcl3	- Basic	Local Alignment	Search Tool client

SYNOPSIS
       blastcl3	 [-]  [-A N]  [-C x]  [-D N]  [-E N] [-F str] [-G N] [-I] [-J]
       [-K N] [-L start,stop] [-M str] [-O filename]  [-Q N]  [-R]  [-S]  [-T]
       [-U]  [-W N]  [-X N] [-Y	X] [-Z N] [-a N] [-b N]	[-d str] [-e X]	[-f X]
       [-g F] [-i filename] [-m	N] [-n]	 [-o filename]	-p str	[-q N]	[-r N]
       [-s] [-t	N] [-u str] [-v	N] [-w N] [-y X] [-z X]

DESCRIPTION
       blastcl3	 accesses  the	newest NCBI BLAST search engine	(version 2.0).
       The software behind BLAST version 2.0 was written from scratch to allow
       BLAST  to  handle the new challenges posed by the sequence databases in
       the coming years.  Updates to this software will	continue in the	coming
       years.

       It  supports  multiple  types  of comparison, governed by the -p	("pro-
       gram") flag:

       blastp	   compares an amino acid query	sequence against a protein se-
		   quence database.

       blastn	   compares  a	nucleotide query sequence against a nucleotide
		   sequence database.

       blastx	   compares the	six-frame conceptual translation products of a
		   nucleotide  query sequence (both strands) against a protein
		   sequence database.

       psitblastn  compares a protein query sequence against a nucleotide  se-
		   quence  database  dynamically translated in all six reading
		   frames (both	strands) using a position specific matrix cre-
		   ated	by PSI-BLAST.

       tblastn	   compares  a protein query sequence against a	nucleotide se-
		   quence database dynamically translated in all  six  reading
		   frames (both	strands).

       tblastx	   compares  the  six-frame translations of a nucleotide query
		   sequence against the	six-frame translations of a nucleotide
		   sequence database.

OPTIONS
       A summary of options is included	below.

       -      Print usage message

       -A N   Multiple	Hits window size; generally defaults to	0 (for single-
	      hit extensions), but defaults to	40  when  using	 discontiguous
	      templates.

       -C X   Use composition-based statistics for blastp or tblastn:
	      T, t, D, or d
		     Default (equivalent to 1)
	      0, F, or f
		     No	composition-based statistics
	      1	     Composition-based statistics as in	NAR 29:2994-3005, 2001
	      2	     Composition-based	score  adjustment as in	Bioinformatics
		     21:902-911, 2005, conditioned on sequence properties
	      3	     Composition-based score adjustment	as  in	Bioinformatics
		     21:902-911, 2005, unconditionally
	      When  enabling statistics	in blastall, blastall_old, or blastcl3
	      (i.e., not ), appending u	(case-insensitive) to the mode enables
	      use of unified p-values combining	alignment and compositional p-
	      values in	round 1	only.

       -D N   Translate	sequences in the database according to genetic code  N
	      in  /usr/share/ncbi/data/gc.prt  (default	 is 1; only applies to
	      tblast*)

       -E N   Extending	a gap costs N (-1 invokes default behavior)

       -F str Filter options for DUST or SEG (default is T)

       -G N   Opening a	gap costs N (-1	invokes	default	behavior)

       -I     Show GIs in deflines

       -J     Believe the query	defline

       -K N   Number of	best hits from a region	to keep.  Off by default.   If
	      used a value of 100 is recommended.

       -L start,stop
	      Location on query	sequence.

       -M str Use matrix str (default =	BLOSUM62)

       -O filename
	      Write (ASN.1) sequence alignments	to filename..

       -P N   Set  to  1  for  single-hit mode or 0 for	multiple-hit mode (de-
	      fault).  Does not	apply to blastn.

       -Q N   Translate	  query	  according   to    genetic    code    N    in
	      /usr/share/ncbi/data/gc.prt (default is 1)

       -R     RPS Blast	search

       -S N   Query  strands  to  search  against database for blastn, blastx,
	      tblastx:
	      1	     top
	      2	     bottom
	      3	     both (default)

       -T     Produce HTML output

       -U     Use lower	case filtering for the query sequence

       -W N   Use words	of size	N (length of best perfect match; zero  invokes
	      default behavior -- 11 for blastn	[28 in MegaBlast mode],	3 oth-
	      erwise).

       -X N   X	dropoff	value for gapped alignment (in bits) (zero invokes de-
	      fault  behavior,	which varies with "program": 30	for blastn [20
	      in MegaBlast mode], 0 for	tblastx, and 15	for everything else.)

       -Y X   Effective	length of the search space  (use  zero	for  the  real
	      size)

       -Z N   X	 dropoff  value	for final [dynamic programming?] gapped	align-
	      ment in bits (default is 50 for blastn, 0	for  tblastx,  25  for
	      others)

       -a N   Number of	threads	to use (default	is one)

       -b N   Number of	database sequences to show alignments for (B) (default
	      is 250)

       -d str Database to use (default is nr)

       -e X   Expectation value	(E) (default = 10.0)

       -f X   Threshold	for extending hits, default if zero: 0 for blastn,  11
	      for blastp, 12 for blastx, and 13	for tblastn and	tblastx.

       -g F   Do not perform gapped alignment (N/A for tblastx)

       -i filename
	      Read query sequence or set from filename (default	is stdin)

       -m N   alignment	view options:
	      0	     pairwise (default)
	      1	     query-anchored showing identities
	      2	     query-anchored, no	identities
	      3	     flat query-anchored, show identities
	      4	     flat query-anchored, no identities
	      5	     query-anchored, no	identities and blunt ends
	      6	     flat query-anchored, no identities	and blunt ends
	      7	     XML Blast output
	      8	     tabular
	      9	     tabular with comment lines
	      10     ASN.1 text
	      11     ASN.1 binary

       -n     MegaBlast	search

       -o filename
	      Write final alignment report to filename rather than stdout

       -p str Use  the	"program" (comparison type) str.  The DESCRIPTION sec-
	      tion covers this option in more detail.

       -q N   Penalty for a nucleotide mismatch	(blastn	only) (default = -3)

       -r N   Reward for a nucleotide match (blastn only) (default = -10)

       -s     Compute locally optimal Smith-Waterman alignments	 (only	avail-
	      able in gapped tblastn mode).

       -t N   Length  of a discontiguous word template (the largest intron al-
	      lowed in a translated nucleotide sequence	when linking  multiple
	      distinct assignments; default = 0; negative values disable link-
	      ing.)

       -u str Restrict search of database to results of	Entrez2	lookup

       -v N   Number of	one-line descriptions to show (V) (default = 500)

       -w N   Frame shift penalty (OOF algorithm for blastx)

       -y X   X	dropoff	for ungapped extensions	in bits	(0.0  invokes  default
	      behavior:	20 for blastn [10 in MegaBlast mode], 7	otherwise).

       -z N   Effective	length of the database (use zero for the real size)

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       <http://blast.ncbi.nlm.nih.gov/>.

NCBI				  2016-09-01			   BLASTCL3(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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