]> BLAST 1.5.3 Paracel version Altschul, Madden, Schaeffer, Zhang, Miller, Lipman Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. http://bioweb.pasteur.fr/docs/softgen.html#BLAST2 blastpar &blast_init; blastpar Blast program perl "pb --quiet blastall -p $value" blastp 1 blastn blastp blastx tblastn tblastx psitblastn The five BLAST programs described here perform the following tasks: . blastp compares an amino acid query sequence against a protein sequence 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; . tblastn compares a protein query sequence against a nucleotide sequence 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. psitblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands) using a position specific matrix created by PSI-BLAST. query Sequence File perl " -i $query" 3 8 seqfile perl 1 start_region Start of required region in query sequence (-L) end_region End of required region in query sequence (-L) perl (defined $value) ? " -L \"$start_region $value\"": " -L $start_region" perl $start_region 5 protein_db protein db perl " -d $value" uniprot 2 uniprot nrprot genpept genpept_new Choose a protein db for blastp or blastx. perl $blastpar =~ /^blast[px]/ nucleotid_db nucleotid db perl " -d $value" embl embl 3 choose a nucleotide db for blastn, tblastn or tblastx perl $blastpar =~ /^blastn|tblast[nx]$/ filter_opt Filtering and masking options 4 BLAST 2.0 and 2.1 uses the dust low-complexity filter for blastn and seg for the other programs. Both 'dust' and 'seg' are integral parts of the NCBI toolkit and are accessed automatically. If one uses '-F T' then normal filtering by seg or dust (for blastn) occurs (likewise '-F F' means no filtering whatsoever). This options also takes a string as an argument. One may use such a string to change the specific parameters of seg or invoke other filters. Please see the 'Filtering Strings' section (below) for details. filter Filter query sequence (DUST with blastn, SEG with others) (-F) perl ($value) ? "" : " -F F" 1 4 other_filters Filtering options (-F must be true) The -F argument can take a string as input specifying that seg should be run with certain values or that other non-standard filters should be used. A coiled-coiled filter, based on the work of Lupas et al. (Science, vol 252, pp. 1162-4 (1991)) written by John Kuzio (Wilson et al., J Gen Virol, vol. 76, pp. 2923-32 (1995)), may be invoked specifying: -F 'C' One may also run both seg and coiled-coiled together by using a ';': -F 'C;S' Filtering by dust may also be specified by: -F 'D' It is possible to specify that the masking should only be done during the process of building the initial words by starting the filtering command with 'm', e.g.: -F 'm S' which specifies that seg (with default arguments) should be used for masking, but that the masking should only be done when the words are being built. If the -U option (to mask any lower-case sequence in the input FASTA file) is used and one does not wish any other filtering, but does wish to mask when building the lookup tables then one should specify: -F 'm' 4 v1 v2 v3 v4 v5 v1 " -F \"m S\"" v2 " -F C" v3 " -F \"C;S\"" v4 " -F D" v5 " -F m" lower_case Use lower case filtering (-U) perl ($value)? " -U T" : "" 0 4 This option specifies that any lower-case letters in the input FASTA file should be masked. selectivity_opt Selectivity options 5 The programs blastn and blastp offer fully gapped alignments. blastx and tblastn have 'in-frame' gapped alignments and use sum statistics to link alignments from different frames. tblastx provides only ungapped alignments. Expect Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e) perl (defined $value && $value != $vdef)? " -e $value":"" 10 5 The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable. word_size Word Size (-W) (zero invokes default behavior) perl (defined $value) ? " -W $value" : "" dist_hits Multiple Hits window size (zero for single hit algorithm) (-A) perl (defined $value) ? " -A $value" : "" extend_hit Threshold for extending hits (-f) perl ($value)? " -f $value":"" Blast seeks first short word pairs whose aligned score reaches at least this value (default for blastp is 11) (T in the NAR paper and in Blast 1.4) dropoff_extent X dropoff for blast extention in bits (0.0 invokes default behavior) (-y) perl (defined $value) ? " -y $value" : "" keep_hits Number of best hits from region to keep (-K) perl (defined $value) ? " -K $value" : "" If this option is used a value of 100 is recommended. gapped_alig Perform gapped alignment (not available with tblastx) (-g) perl ($value)? "": " -g F" 1 perl $blastpar ne "tblastx" dropoff X dropoff value for gapped alignment (in bits) (-X) perl (defined $value)? " -X $value":"" This is the value that control the path graph region explored by Blast during a gapped extension (Xg in the NAR paper) (default for blastp is 15). dropoff_final X dropoff value for final alignment (in bits) (-Z) perl (defined $value) ? " -Z $value" : "" scoring_opt Scoring options 4 mismatch Penalty for a nucleotide mismatch (blastn) (-q) perl (defined $value && $value != $vdef)? " -q $value":"" -3 perl $blastpar eq "blastn" match Reward for a nucleotide match (blastn) (-r) perl (defined $value && $value != $vdef)? " -r $value":"" 1 perl $blastpar eq "blastn" matrix Matrix (-M) perl (defined $value && $value ne $vdef)? " -M $value" : "" BLOSUM62 BLOSUM62 BLOSUM45 BLOSUM80 PAM30 PAM70 perl $blastpar ne "blastn" open_a_gap Cost to open a gap (-G) perl (defined $value)? " -G $value":"" default is 5 for blastn, 10 for blastp, blastx and tblastn extend_a_gap Cost to extend a gap (-E) perl (defined $value)? " -E $value":"" 5 default is 2 for blastn, 1 for blastp, blastx and tblastn Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are: Existence Extension 10 1 10 2 11 1 8 2 9 2 (source: NCBI Blast page) translation_opt Translation options gc_query Query Genetic code to use (blastx) (-Q) perl (defined $value && $value != $vdef)? " -Q $value":"" 1 4 1 2 3 4 5 6 9 10 11 12 13 14 15 perl $blastpar =~ /blastx$/ gc_db DB Genetic code (for tblast[nx] only) (-D) perl ($value != $vdef) ? " -D $value":"" 1 4 1 2 3 4 5 6 9 10 11 12 13 14 15 perl $blastpar =~ /^tblast/ strand Query strand to search against database (for blastx and tblastx) (-S) perl ($value && $value != $vdef) ? " -S $value" : "" 3 1 2 3 perl $blast =~ /blastx$/ affichage Report options Descriptions How many short descriptions? (-v) perl (defined $value && $value != $vdef)? " -v $value":"" 500 5 Maximum number of database sequences for which one-line descriptions will be reported (-v). Alignments How many alignments? (-b) perl (defined $value && $value != $vdef)? " -b $value":"" 250 5 Maximum number of database sequences for which high-scoring segment pairs will be reported (-b). view_alignments Alignment view options (not with blastx/tblastx) (-m) perl ($value)? " -m $value" : "" 0 4 0 1 2 3 4 5 6 7 8 perl $blastpar !~ /blastx$/ show_gi perl $protein_db eq "nrprot" Show GI's in deflines (only available for NCBI db such as nrprot) (-I) perl ($value)? " -I" : "" 0 4 Causes NCBI gi identifiers to be shown in the output, in addition to the accession and/or locus name. Warning: only available for NCBI db such as nrprot. seqalign_file SeqAlign file (-J option must be true) (-O) perl ($value)? " -O $value" : "" 4 SeqAlign is in ASN.1 format, so that it can be read with NCBI tools (such as sequin). This allows one to view the results in different formats. perl $believe believe Believe the query defline (-J) perl ($value)? " -J":"" 0 4 htmloutput Html output 1 perl ($_html) && ($view_alignments !~ /^[78]$/) perl ($value)? " && html4blast -o blast.html -g" : "" 20 htmlopt HTML output options (html4blast) perl $htmloutput && ($_html) && ($view_alignments !~ /^[78]$/) html4blast_input perl " blast.txt" 30 external_links Use external web sites for databases entries retrieval links (-e instead of -s) 0 25 perl ($value)? " -e" : " -s" 25 -s option will use SRS for databases entries retrieval links, whereas -e will use the original database site links. one_HSP_per_line Draw one HSP per line in image instead of putting all HSP in one line (-l) 0 25 perl ($value)? " -l" : "" 25 Useful for genomes searching, where there is only one sequence in the database. image_query Generate images names based on corresponding query (-q) 0 25 perl ($value)? " -q" : "" 25 Useful when you only want to keep the image. htmlfile blast.html othersopt Other Options 5 restrict_db perl $protein_db eq "nrprot" Restrict search of database to GI's in file (-l) perl (defined $value) ? " -l $value" : "" 7 psi_checkpoint PSI-TBLASTN checkpoint file (-R) perl (defined $value) ? " -R $value" : "" perl $blastpar eq psitblastn psiblast_matrix perl 1 psiblast_matrix query txtoutput perl " > blast.txt" perl $view_alignments !~ 7 7 tmp_outfile blast.txt blast_output perl $view_alignments !~ [78] xmloutput perl " > blast.xml" perl $view_alignments =~ 7 blast.xml 7