FASTS/TFASTSv3(1)

✨ FASTS/TFASTSv3(1) — General Commands Manual ✨

okay bestie, welcome to the FASTS/TFASTSv3 manual, this one is genuinely iconic 💖 it lives in section 1 of the manual (general commands, the ones you just type), and it's your girl's guide to comparing a whole lil squad of short peptides against a database. let's go 🫶

🌸 NAME 🌸

fasts3, fasts3_t — compare several short peptide sequences against a protein database using a modified fasta algorithm.

tfasts3, tfasts3_t — compare short peptides against a translated DNA database.

🦋 DESCRIPTION 🦋

so fasts3 and tfasts3 are designed to compare a set of peptides — presumably non-contiguous ones, like they don't have to sit next to each other at all — against a protein database (fasts3) or a translated DNA database (tfasts3). they are designed particularly for short peptide data coming out of mass-spec analysis of protein digests. 🧪✨

and here's the vibe check: the traditional fasta3 search takes a protein or DNA sequence, but fasts3 and tfasts3 are built different 💅 they work with a query sequence shaped like this:

>tests from mgstm1
MLLE,
MILGYW,
MGADP,
MLCYNP

that sequence is telling you four peptides are gonna be used. and when you compare this sequence against mgstm1.aa (which comes with the distribution, no cap), the result is:

 testf    MILGYW----------MLLE------------MGDAP-----------
          ::::::          ::::            :::::
 GT8.7  MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
                10        20        30        40        50

 testf  --------------------------------------------------

 GT8.7  FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
                60        70        80        90       100

                       20
 testf  ------------MLCYNP
                    ::::::
 GT8.7  ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
               110       120       130       140       150

ate. no crumbs. 🔥

💅 Options 💅

okay so both fasts3 and tfasts3 can take a query sequence straight from the unix "stdin" data stream. this makes it so much easier to use fasta3 and its relatives as part of a WWW page. to say "yeah use stdin please", pass "-" 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. this enables checks on sequence alphabet that cause problems with tfastx3, tfasty3, tfasta3.
• -E # — Expectation value limit for displaying scores and alignments. heads up bestie: expectation values for fasts3 and tfasts3 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 0,1,2,3,4,5,6,9,10 — alignment display options
• -N # — break long library sequences into blocks of # residues. useful for bacterial genomes, which have only one sequence entry. -N 2000 works 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 — tfasts3 can use the BLAST translation 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.
• -3 — (TFASTS3 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, you're literally a peptide-searching main character now. periodt. 🎀

this page is from the local source, version FASTS/TFASTSv3, filed under section 1 of the manual. go forth and align. 💜✨