]> 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 megablastpar &blast_init; megablastpar perl "pb --quiet megablast" 1 query DNA Sequence File perl " -i $query" 3 8 seqfile perl 1 nucleotid_db nucleotid db perl not $list_of_GI perl " -d $value" embl genbank genbank: Genbank last release + updates genbank_new genbank_new: Genbank updates 3 filter_opt Filtering, masking and other input 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. 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 $start_region 5 filter Filter query sequence (DUST with blastn, SEG with others) (-F) perl ($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 masking instead of filtering (with Seg) v2 coiled-coiled filter v3 both seg and coiled-coiled filters v4 dust filter (DNA query) v5 lower-case masking (-U must be true) 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 ($value)? " -U T" : "" 0 4 This option specifies that any lower-case letters in the input FASTA file should be masked. masked_query_output Masked query output (-Q) perl ($value)? " -Q query.masked" : "" 0 4 query_strand Query strands to search against database (-S) perl ($value && $value != $vdef)? " -S $value" : "" 1 top 2 bottom 3 both 3 4 selectivity_opt Selectivity options 5 The programs blastn offers fully gapped 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. 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 dynamic programming gapped extension (-Z) perl (defined $value && $value != $vdef) ? " -Z $value" : "" 50 dropoff_extent X dropoff value for ungapped extension (-y) perl (defined $value && $value != $vdef) ? " -y $value" : "" 10 ident_cutoff Identity percentage cut-off (-p) perl (defined $value && $value != $vdef) ? " -p $value" : "" 0 word_size Word Size (length of best perfect match) (-W) perl (defined $value && $value != $vdef) ? " -W $value" : "" 28 word_len Length of a discontiguous word template (contiguous word if 0) (-t) perl (defined $value && $value != $vdef) ? " -t $value" : "" 0 word_type Type of a discontiguous word template (-N) perl ($value)? " -N $value" : "" 0 4 0 0 - coding 1 1 - optimal 2 2 - two simultaneous dist_hits Multiple Hits window size (zero for single hit algorithm) (-A) perl (defined $value) ? " -A $value" : "" keep_hits Number of best hits from region to keep (-K) perl (defined $value) ? " -K $value" : "" If this option is used a value of 100 is recommended. greedy Use non-greedy (dynamic programming) extension for affine gap scores (-n) perl ($value)? " -n" : "" 0 4 scoring_opt Scoring options 4 mismatch Penalty for a nucleotide mismatch (-q) perl (defined $value && $value != $vdef)? " -q $value":"" -3 match Reward for a nucleotide match (-r) perl (defined $value && $value != $vdef)? " -r $value":"" 1 open_a_gap Cost to open a gap (-G) perl (defined $value)? " -G $value":"" default is 5 extend_a_gap Cost to extend a gap (-E) perl (defined $value)? " -E $value":"" 5 default is 2 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) alig_nb The number of alignments to report per db subject (0 means no limit) (-u) perl (defined $value && $value != $vdef)? " -u $value":"" 0 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). min_hit_score Minimal hit score to report (-s) perl (defined $value && $value != $vdef)? " -s $value":"" 0 5 Maximum number of database sequences for which high-scoring segment pairs will be reported (-b). output_type Type of output (-D) perl ($value)? " -D $value" : "" 0 4 0 0 - alignment endpoints and score 1 1 - all ungapped segments endpoints 2 2 - traditional BLAST output 3 3 - tab-delimited one line format [Integer] view_alignments perl $output_type eq "2" Alignment view options (traditional BLAST output) (-m) perl ($value)? " -m $value" : "" 0 4 0 0: pairwise 1 1: query-anchored showing identities 2 2: query-anchored no identities 3 3: flat query-anchored, show identities 4 4: flat query-anchored, no identities 5 5: query-anchored no identities and blunt ends 6 6: flat query-anchored, no identities and blunt ends 7 7: XML Blast output 8 8: Tabular output 9 9: tabular with comment lines 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. show_full_id Show full IDs in the output (default - only GIs or accessions) (-f) perl ($value)? " -f" : "" 0 4 report_log Report the log information at the end of output (-R) perl ($value)? " -R" : "" 0 4 seqalign_file ASN.1 SeqAlign file (traditional BLAST output) (-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 $output_type eq "2" believe Believe the query defline (-J) perl ($value)? " -J":"" 0 4 htmloutput Html output (html4blast) 1 perl ($_html) && ($output_type == 2) && ($view_alignments !~ /^[78]$/) perl ($value)? " && html4blast -o megablast.html -g" : "" 20 htmlopt HTML output options (html4blast) perl $htmloutput && ($_html) && ($output_type == 2) && ($view_alignments !~ /^[78]$/) html4blast_input perl " megablast.txt" 30 external_links Use external web sites for databases entries retrieval links (-e instead of -s) 0 25 perl ($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 megablast.html other_opt Other options 4 queries_len Maximal total length of queries for a single search (-M) perl (defined $value && $value != $vdef)? " -M $value" : "" 20000000 db_len Effective length of the database (-z) perl (defined $value && $value != $vdef)? " -z $value" : "" 0 hash_pos Maximal number of positions for a hash value (set to 0 to ignore) (-P) perl (defined $value && $value != $vdef)? " -P $value" : "" 0 list_of_GI Restrict search of database to list of GI's (-l) perl ($value && ($value !~ /,/ || $value =~ s/,/ /g) )? " -l \\"$value\\" " : "" 3 gen_words Generate words for every base of the database (default is every 4th base) (-g) perl ($value)? " -g" : "" 0 txtoutput perl " > megablast.txt" perl $view_alignments !~ 7 7 tmp_outfile megablast.txt blast_output perl $view_alignments !~ [78] masked_query_outfile query.masked xmloutput perl " > megablast.xml" perl $view_alignments =~ 7 megablast.xml 7