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FASTF/TFASTFv3(1)	    General Commands Manual	     FASTF/TFASTFv3(1)

       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	trans-
       lated DNA database.

       fastf3 and tfastf3 are designed to compare a sequence of	mixed peptides
       to a protein (fastf3) or	translated DNA (tfastf3) database.  Unlike the
       traditional fasta3 search, which	uses a protein or DNA sequence,	fastf3
       and tfastf3 work	with a query sequence of the form:
	    >testf from	mgstm1
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
position '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 deconvolved to form:
     testf    MILGY-----------MLLEY-----------MGDAP-----------
	      :::::	      :::::	      :::::
		    10	      20	30	  40	    50

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

		    60	      70	80	  90	   100

     testf  ------------MLCYN
		   110	     120       130	 140	   150

       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.
	      Expectation 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  se-

       -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 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	- tfastf3 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-

       -1     Sort by "init1" score.

       -3     (TFASTF3 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		     FASTF/TFASTFv3(1)

NAME | DESCRIPTION | Options | Environment variables: | AUTHOR

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