FASTF/TFASTFv3(1) General Commands Manual FASTF/TFASTFv3(1) NAME fastf3, fastf3_t - compare a mixed peptide sequence against a protein data- base using a modified fasta algorithm. tfastf3, tfastf3_t - compare a mixed pepide sequence against a translated DNA database. DESCRIPTION fastf3 and tfastf3 are designed to compare a sequence of mixed peptides to a protein (fastf3) or translated DNA (tfastf3) database. Unlike the tradi- tional fasta3 search, which uses a protein or DNA sequence, fastf3 and tfastf3 work with a query sequence of the form: >testf from mgstm1 MGCEN, MIDYP, MLLAY, MLLGY This sequence indicates that a mixture of four peptides has been found, with 'M' in the first position of each one (as from a CNBr cleavage), in the second posi- tion 'G', 'I', or 'L' (twice), at the third position 'C', 'D', or 'L' (twice), at the fourth position 'E', (included with the distribution), the mixture is de- convolved to form: testf MILGY-----------MLLEY-----------MGDAP----------- ::::: ::::: ::::: GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK 10 20 30 40 50 testf -------------------------------------------------- GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV 60 70 80 90 100 20 testf ------------MLCYN ::::: GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG 110 120 130 140 150 Options fastf3 and tfastf3 can accept a query sequence from the unix "stdin" data stream. This makes it much easier to use fasta3 and its relatives as part of a WWW page. To indicate that stdin is to be used, use "-" or "@" as the query sequence file name. -b # number of best scores to show (must be < -E cutoff) -d # number of best alignments to show ( must be < -E cutoff) -D turn on debugging mode. Enables checks on sequence alphabet that cause problems with tfastx3, tfasty3, tfasta3. -E # Expectation value limit for displaying scores and alignments. Ex- pectation values for fastf3 and tfastf3 are not as accurate as those for the other fasta3 programs. -H turn off histogram display -i compare against only the reverse complement of the library sequence. -L report long sequence description in alignments -m 0,1,2,3,4,5,6,10 alignment display options -n force query to nucleotide sequence -N # break long library sequences into blocks of # residues. Useful for bacterial genomes, which have only one sequence entry. -N 2000 works well for well for bacterial genomes. -O file send output to file -q/-Q quiet option; do not prompt for input -R file save all scores to statistics file -S # offset substitution matrix values by a constant # -s name specify substitution matrix. BLOSUM50 is used by default; PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120, P250, or BL62. With this version, many more scoring matrices are available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10, M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be specified. -T # (threaded, parallel only) number of threads or workers to use (set by default to 4 at compile time). -t # Translation table - tfastf3 can use the BLAST tranlation tables. See http://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/. -w # line width for similarity score, sequence alignment, output. -x "#,#" offsets query, library sequence for numbering alignments -z # Specify statistical calculation. Default is -z 1, which uses regres- sion against the length of the library sequence. -z 0 disables sta- tistics. -z 2 uses the ln() length correction. -z 3 uses Altschul and Gish's statistical estimates for specific protein BLOSUM scoring matrices and gap penalties. -z 4: an alternate regression method. -Z db_size Set the apparent database size used for expectation value calcula- tions. -1 Sort by "init1" score. -3 (TFASTF3 only) use only forward frame translations Environment variables: FASTLIBS location of library choice file (-l FASTLIBS) SMATRIX default scoring matrix (-s SMATRIX) SRCH_URL the format string used to define the option to re-search the data- base. REF_URL the format string used to define the option to lookup the library sequence in entrez, or some other database. AUTHOR Bill Pearson wrp@virginia.EDU local FASTF/TFASTFv3(1)
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