Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
FASTS/TFASTSv3(1)	    General Commands Manual	     FASTS/TFASTSv3(1)

       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

       fasts3  and tfasts3 are designed	to compare set of (presumably non-con-
       tiguous)	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	tradi-
       tional  fasta3 search, which uses a protein or DNA sequence, fasts3 and
       tfasts3 work with a query sequence of the form:
	    >tests from	mgstm1
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-----------
	      ::::::	      ::::	      :::::
		    10	      20	30	  40	    50

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

		    60	      70	80	  90	   100

     testf  ------------MLCYNP
		   110	     120       130	 140	   150

       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 se-

       -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  ma-
	      trices  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.

       -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 re-
	      gression	against	 the length of the library sequence. -z	0 dis-
	      ables statistics.	 -z 2 uses the ln() length  correction.	 -z  3
	      uses Altschul and	Gish's statistical estimates for specific pro-
	      tein BLOSUM scoring matrices and gap penalties. -z 4: an	alter-
	      nate regression method.

       -Z db_size
	      Set the apparent database	size used for expectation value	calcu-

       -3     (TFASTS3 only) use only forward frame translations

Environment variables:
	      location of library choice file (-l FASTLIBS)

	      default scoring matrix (-s SMATRIX)

	      the format string	used to	define the  option  to	re-search  the

	      the  format  string  used	to define the option to	lookup the li-
	      brary sequence in	entrez,	or some	other database.

       Bill Pearson

				     local		     FASTS/TFASTSv3(1)

NAME | DESCRIPTION | Options | Environment variables: | AUTHOR

Want to link to this manual page? Use this URL:

home | help