---
name: "fasts3"
section: "1"
platform: "linux"
package: "fasta3"
version: "36.3.8i.14-Nov-2020-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fasts3"
---

# fasts3(1)

compare several short peptide sequences against a protein database using a modified fasta algorithm. tfasts3, tfasts3\_t - compare short pepides against a translated DNA database.

## NAME

fasts3, fasts3\_t - compare several short peptide sequences against a protein database using a modified fasta algorithm.

tfasts3, tfasts3\_t - compare short pepides against a translated DNA database.

## DESCRIPTION

**fasts3** and **tfasts3** are designed to compare set of (presumably non-contiguous) peptides to a protein (fasts3) or translated DNA (tfasts3) database. fasts3/tfasts3 are designed particularly for short peptide data from mass-spec analysis of protein digests.  Unlike the traditional **fasta3** search, which uses a protein or DNA sequence, **fasts3** and **tfasts3** work with a query sequence of the form:

```
>tests from mgstm1
MLLE,
MILGYW,
MGADP,
MLCYNP
```

This sequence indicates that four peptides are to be used.  When this sequence is compared against mgstm1.aa (included with the distribution), 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
```

## Options

**fasts3** and **tfasts3** 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.  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 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 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.

- \-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