]> 34t10d3 Sequence database search (version 3) W. Pearson Pearson, W. R. (1999) Flexible sequence similarity searching with the FASTA3 program package. Methods in Molecular Biology W. R. Pearson and D. J. Lipman (1988), Improved Tools for Biological Sequence Analysis, PNAS 85:2444-2448 W. R. Pearson (1998) Empirical statistical estimates for sequence similarity searches. In J. Mol. Biol. 276:71-84 Pearson, W. R. (1996) Effective protein sequence comparison. In Meth. Enz., R. F. Doolittle, ed. (San Diego: Academic Press) 266:227-258 fasta fasta Fasta program perl "$value -q" fasta_t 0 fasta_t fasta: protein or DNA query vs similar db (FASTA release 3.0) tfasta_t tfasta: protein query vs translated DNA db fastx_t fastx: DNA query (translated, 3 frames) vs protein db (frameshifts only between codons) tfastx_t tfastx: protein query vs translated DNA db (frameshifts only between codons) fasty_t fasty = fastx + frameshifts anywhere tfasty_t tfasty = tfastx + frameshifts anywhere fastf_t fastf: mixed peptide seq vs protein db (modified algorithm) tfastf_t tfastf: mixed peptide seq vs translated DNA db (modified algorithm) fasts_t fasts: several short peptide seq vs protein db (modified algorithm) tfasts_t tfasts: several short peptide seq vs translated DNA db (modified algorithm) . fasta - scan a protein or DNA sequence library for similar sequences . tfasta - compare a protein sequence to a DNA sequence librarSy, translating the DNA sequence library `on-the-fly' to the 3 forward and the 3 reverse frames without framshifts. . fastx/fasty - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in three frames, with frameshifts. fasty2 allows frameshifts inside codons. . tfastx/tfasty - compare a protein sequence vs a translated DNA db, with frameshifts. tfasty allows frameshifts inside codons. . fastf/tfastf - compare an ordered peptide mixture (obtained for example by Edman degradation of a CNBr cleavage) against a protein or translated DNA database. . fasts/tfasts - compare a set of short peptide fragments (obtainded from a mass-spec analysis of a protein) against a protein or translated DNA database. query Query sequence File perl " $value" 2 8 seqfile perl 1 seqtype Is it a DNA or protein sequence (-n) perl (($fasta =~ /^fasta/ && $value eq "DNA") || $fasta =~ /^fast(x|y)/) ? " -n" : "" 1 DNA DNA protein protein fastf and fasts take a protein sequence perl $fasta =~ /^fast(f|s)/ && $seqtype eq "DNA" fastx and fasty take a DNA sequence perl $fasta =~ /^fast(x|y)/ && $seqtype eq "protein" tfasta, tfastx, tfasty, tfastf and tfasts take a protein sequence perl $fasta =~ /^tfast/ && $seqtype eq "DNA" protein_db Protein Database perl &fastapath; uniprot 3 &protdbs; perl ($seqtype eq "protein" && $fasta =~ /^fasta/) || $fasta =~ /^fast(x|y|s|f)/ nucleotid_db Nucleotid Database perl &fastapath; embl 3 &nucdbs; perl ($seqtype eq "DNA" && $fasta =~ /^fasta/ ) || $fasta =~ /^tfast/ break_long Break long library sequences into blocks (-N) perl (defined $value) ? " -N $value" : "" slectivity_opt Selectivity options 1 ktup ktup : sensitivity and speed of the search (protein:2, DNA:6) perl (defined $value)? " $value":"" 4 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). optcut OPTCUT : the threshold for optimization. (-c) perl (defined $value)? " -c $value":"" The OPTCUT value is normally calculated based on sequence length. gapinit Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f) perl (defined $value)? " -f $value":"" The default for fastx/fasty/tfastz/tfasty is -15. gapext Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g) perl (defined $value)? " -g $value":"" The default for fastx/fasty/tfastz/tfasty is -3. high_expect Maximal expectation value threshold for displaying scores and alignments (-E) perl (defined $value && $value != $vdef)? " -E $value":"" 10.0 Expectation value limit for displaying scores and alignments. Typically 10.0 for protein sequence comparisons; 5.0 for fastx, and 2.0 for DNA sequence comparisons. low_expect Minimal expectation value threshold for displaying scores and alignments (-F) perl (defined $value) ? " -F $value":"" This allow one to skip over close relationships in searches for more distant relationships. score_opt Scoring options 1 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 X_penalty Penalty for a match to 'X' (independently of the PAM matrix) (-x) perl (defined $value) ? " -x $value" : "" Particularly useful for fast[xy], where termination codons are encoded as 'X'. frame_transl_opt Frameshift and translation options 1 frameshift Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h) perl (defined $value)? " -h $value":"" perl ($fasta =~ /fast(x|y)/) frameshift_within Penalty for frameshift within a codon (fasty/tfasty)(-j) perl (defined $value)? " -j $value":"" perl ($fasta =~ /fasty/) threeframe Search only the three forward frames (tfasta) (-3) perl ($value) ? " -3":"" perl $fasta =~ /^tfasta/ invert Reverse complement the query sequence (all tfasta) (-i) perl ($value) ? " -i" : "" perl $fasta =~ /^tfasta/ genetic_code Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t) perl ($value != $vdef) ? " -t $value" : "" 1 1 1: Standard 2 2: Vertebrate Mitochondrial 3 3: Yeast Mitochondrial 4 4: Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5 5: Invertebrate Mitochondrial 6 6: Ciliate Macronuclear and Dasycladacean 9 9: Echinoderm Mitochondrial 10 10: Euplotid Nuclear 11 11: Bacterial 12 12: Alternative Yeast Nuclear 13 13: Ascidian Mitochondrial 14 14: Flatworm Mitochondrial 15 15: Blepharisma Macronuclear perl $fasta =~ /^tfast/ || $fasta =~ /fast[xy]/ optimize_opt Optimization options 1 band band-width used for optimization (-y) perl (defined $value)? " -y $value":"" Set the band-width used for optimization. -y 16 is the default for protein when ktup=2 and for all DNA alignments. -y 32 is used for protein and ktup=1. For proteins, optimization slows comparison 2-fold and is highly recommended. swalig unlimited Smith-Waterman alignment for DNA (-A) perl ($value)? " -A":"" force Smith-Waterman alignment for output. Smith-Waterman is the default for protein sequences and FASTX, but not for TFASTA or DNA comparisons with FASTA. noopt no limited optimization (-o) perl ($value)? " -o":"" Turn off default optimization of all scores greater than OPTCUT. Shirt results by 'initn' scores reduces the accuracy of statistical estimates. stat Specify statistical calculation. (-z) perl ($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 $stat > 0 This doubles the time required for a search, but allows accurate statistics to be estimated for libraries comprised of a single protein family. affichage Report options 1 histogram No histogram (-H) perl ($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 ($value) ? " -B" : "" 0 1 z-score 0 bit-score showall both sequences are shown in their entirety in alignments (fasta only) (-a) perl ($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 \"$value\"":"" causes fasta/lfasta/plfasta to start numbering the aligned sequences starting with offset1 and offset2, rather than 1 and 1. This is particularly useful for showing alignments of promoter regions. info Display more information about the library sequence in the alignment (-L) perl ($value)? " -L":"" statfile Write out the sequence identifier, superfamily number, and similarity scores to this file (-R) perl ($value)? " -R $value":"" other_opt Other options 1 filter Lower case filtering (-S) perl ($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 100 mview_input perl 1 fasta.out html_outfile perl " > fasta.html" 100 perl $html_output "fasta.html"