FASTF/TFASTFv3(1)

✨ FASTF/TFASTFv3 — the girlies are searching 💅

okay bestie, so this is the manual for the FASTF family of search tools, fastf3, fastf3_t, tfastf3, and tfastf3_t. we're in the General Commands Manual, and this whole thing is giving "compare a mixed peptide sequence against a database but make it spicy." let's get into it 🫶

🌸 NAME 🌸

fastf3, fastf3_t — compare a mixed peptide sequence against a protein database using a modified fasta algorithm.

tfastf3, tfastf3_t — compare a mixed pepide sequence against a translated DNA database.

(yes, "pepide" is in the original and we are NOT fixing it, that's her little typo, she's iconic ✨)

🦋 DESCRIPTION 🦋

so like, fastf3 and tfastf3 are built to compare a sequence of mixed peptides against a protein database (fastf3) or a translated DNA database (tfastf3). that's the whole vibe.

and here's the thing — the traditional fasta3 search works with a protein or DNA sequence, right? but fastf3 and tfastf3 are not doing that. they take a query sequence that looks like this:

>testf from mgstm1
MGCEN,
MIDYP,
MLLAY,
MLLGY

so what is this telling us?? this sequence means a mixture of four peptides was found, with 'M' sitting in the first position of each one (like from a CNBr cleavage, periodt), and then:

• second position: 'G', 'I', or 'L' (twice, she's popular)
• third position: 'C', 'D', or 'L' (twice, also popular)
• fourth position: 'E', (included with the distribution), the mixture is deconvolved to form:

and the deconvolution looks like this, no cap:

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

like?? the colons are the matches, the dashes are the gaps, it's giving alignment realness 😭💖

✨ Options ✨

fastf3 and tfastf3 can accept a query sequence straight from the unix "stdin" data stream. this is so handy — it makes it way easier to use fasta3 and all her relatives as part of a WWW page. to say "hey, use stdin please", just use "-" or "@" as the query sequence file name. 🎀

• -b # — number of best scores to show (has to be < the -E cutoff, bestie, them's the rules)
• -d # — number of best alignments to show (also has to be < the -E cutoff)
• -D — turn on debugging mode. this enables checks on the sequence alphabet that cause problems with tfastx3, tfasty3, tfasta3. 💀
• -E # — Expectation value limit for displaying scores and alignments. heads up tho: the Expectation values for fastf3 and tfastf3 are not as accurate as the ones for the other fasta3 programs. she's doing her best okay 😭
• -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. super useful for bacterial genomes, which have only one sequence entry. -N 2000 works well for well for bacterial genomes. (the double "for well for well" is hers, we love her 🙈)
• -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. the matrix menu is lowkey stacked 🔥
• -T # — (threaded, parallel only) number of threads or workers to use (set by default to 4 at compile time). parallel girlies rise up 👑
• -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 regression against the length of the library sequence. -z 0 disables statistics. -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 calculations
• -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 database
• 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

and that's the whole page, bestie 💖 this is the local build of FASTF/TFASTFv3, section 1 of the General Commands Manual, and she's been sitting here in the manual pages holding it down. go forth and align, you absolute main character 🦋👑💅