]> 3.4t20 Sequence database search (version 3) W. Pearson Pearson, W. R. (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11: 635-650 Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197 http://bioweb.pasteur.fr/docs/softgen.html#FASTA ssearch ssearch_expl ssearch: protein or DNA query vs similar db ssearch - scan a protein or dna sequence library for similar sequences using the Smith and Waterman algorithm. ssearch perl "ssearch -q" ssearch34_t 0 query Query sequence File perl " $value" 10 8 seqfile perl 1 seqtype Is it a DNA or protein sequence (-n) perl ($value eq "DNA") ? " -n" : "" 1 DNA DNA protein protein protein_db Protein Database perl &fastapath; sptrnrdb 20 &protdbs; perl $seqtype eq "protein" Please note that Swissprot usage by and for commercial entities requires a license agreement. nucleotid_db Nucleotid Database perl &fastapath; embl 20 &nucdbs; perl $seqtype eq "DNA" slectivity_opt Selectivity options 1 ktup ktup : sensitivity and speed of the search (protein:2, DNA:6) perl (defined $value)? " $value":"" 30 ktup sets the sensitivity and speed of the search. If ktup=2, similar regions in the two sequences being compared are found by looking at pairs of aligned residues; if ktup=1, single aligned amino acids are examined. ktup can be set to 2 or 1 for protein sequences, or from 1 to 6 for DNA sequences. The default if ktup is not specified is 2 for proteins and 6 for DNA. 1ktup=1 should be used for oligonucleotides (DNA query length < 20). gapinit Penalty for gap initiation (-12 by default for ssearch with proteins, -16 for DNA) (-f) perl (defined $value)? " -f $value":"" 4 gapext Penalty for gap extention (-2 by default for ssearch with proteins, -4 for DNA) (-g) perl (defined $value)? " -g $value":"" 4 score_opt Scoring options 4 nucleotid_match Reward for a nucleotid match (-r) +5 nucleotid_mismatch Penalty for a nucleotid mismatch (-r) -4 perl (defined $value && ($value != $vdef || $dna_match != 5)) ? " -r \"$dna_match/$value\"" : "" perl defined $dna_match '+5/-4' are the default values for nucleotid match/mismatch, but '+3/-2' can perform better in some cases. matrix Scoring matrix file (-s) perl ($value ne $vdef) ? " -s $value" : "" BL50 BL50 BLOSUM50 BL62 BLOSUM62 BL80 BLOSUM80 P20 PAM20 P40 PAM40 P120 PAM120 P250 PAM250 M10 MDM_10 M20 MDM_20 M40 MDM_40 optimize_opt Optimization options 4 stat Specify statistical calculation. (-z) perl ($random && $value > 0) ? " -z 1$value" : ($value != $vdef) ? " -z $value" : "" 1 -1 -1: turn off statistics 0 0: no correction of library sequebce length 1 1: weigthed regression against the length of the library sequence 2 2: maximum likelihood estimates of Lambda abd K 3 3: Altschul-Gish parameters 4 4: Variation1 of 1 5 5: Variation2 of 1 In general, 1 and 2 are the best methods. random Estimate stat parameters from shuffled copies of each library sequence (-z) 0 $stat > 0 This doubles the time required for a search, but allows accurate statistics to be estimated for libraries comprised of a single protein family. affichage Report options 4 histogram No histogram (-H) perl ($value)? " -H":"" scores number of similarity scores to be shown (-b) perl (defined $value)? " -b $value":"" alns number of alignments to be shown (-d) perl (defined $value)? " -d $value":"" html_output HTML output (-m) perl ($value)? " -m 6" : "" 0 markx Alternate display of matches and mismatches in alignments perl ($value && $value != $vdef )? " -m $value" : "" 0 0 0 [: identities] [. conservative repl] [ non-conserv repl] 1 1: [ identities] [x conservative repl] [X non-conserv repl] 2 2: [. identities] [res mismatch] - don't display the 2nd seq 3 3: writes a file of library sequences in FASTA format 4 4: displays a graph of the alignment 9 9: 0 + percent identity + coordinates 10 10: output more information perl ! $html_output (MARKX) =0,1,2,3,4. Alternate display of matches and mismatches in alignments. MARKX=0 uses ':','.',' ', for identities, conservative replacements, and non-conservative replacements, respectively. MARKX=1 uses ' ','x', and 'X'. MARKX=2 does not show the second sequence, but uses the second alignment line to display matches with a '.' for identity, or with the mismatched residue for mismatches. MARKX=2 is useful for aligning large numbers of similar sequences. MARKX=3 writes out a file of library sequences in FASTA format. MARKX=3 should always be used with the 'SHOWALL' (-a) option, but this does not completely ensure that all of the sequences output will be aligned. MARKX=4 displays a graph of the alignment of the library sequence with repect to the query sequence, so that one can identify the regions of the query sequence that are conserved. init1 sequences ranked by the z-score based on the init1 score (-1) perl ($value)? " -1":"" z_score_out Show normalize score as (-B) perl ($value) ? " -B" : "" 0 1 z-score 0 bit-score showall both sequences are shown in their entirety in alignments (-a) perl ($value)? " -a":"" linlen output line length for sequence alignments (max. 200) (-w) perl (defined $value && $value != $vdef)? " -w $value":"" 60 offsets Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X) perl ($value)? " -X \"$value\"":"" causes ssearch to start numbering the aligned sequences starting with offset1 and offset2, rather than 1 and 1. This is particularly useful for showing alignments of promoter regions. info Display more information about the library sequence in the alignment (-L) perl ($value)? " -L":"" statfile Write out the sequence identifier, superfamily number, and similarity scores to this file (-R) perl ($value)? " -R $value":"" other_opt Other options 4 filter Lower case filtering (-S) perl ($value) ? " -S" : "" 0 Treat lower-case characters in the query or library sequence as 'low-complexity' residues. These characters are treated as 'X' during the initial scan, but are treated as normal residues during the final alignment. Sinces statistical significance is calculated from similarity score calculated during library search, low complexity regions will not produce statistical significant matches. If a significant alignment contains low complexity regions the final score may be higher than the score obtainded during the search. outfile mview_input perl 1 100 ssearch.out html_outfile perl " > ssearch.html" 100 perl $html_output "ssearch.html"