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

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-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
	    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 se-
	      quence.

       -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.
	      See		     http://www.ncbi.nih.gov/htbin-post/Taxon-
	      omy/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 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-
	      lations.

       -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 li-
	      brary sequence in	entrez,	or some	other database.

AUTHOR
       Bill Pearson
       wrp@virginia.EDU

				     local		     FASTS/TFASTSv3(1)

NAME | DESCRIPTION | Options | Environment variables: | AUTHOR

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