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NetFETCH

GCG version 10 has introduced a new programs called NetFETCH that retrieves sequences directly from the NCBI's NetENTREZ web server. This insures compatibility with sequence names/numbers found in BLAST and ENTREZ searches.

NetFETCH can be used to retrieve sequences by name or accession number. It also can retrieve multiple sequence by placing a comma between sequence names or accession numbers.

NetFETCH will retrieve an entire list of sequences found in a NetBLAST search. Simply type the name of the NetBLAST output file as input for NetFETCH:

> NetFETCH frag.blastp

The output of NetFETCH is a complete listing of the GenBank acessions including all comment and annotations in a format known as .RSF. This .RSF file can be loaded into SeqLab, or used as input for any GCG program the handles multiple sequences - such as PILEUP.

An .RSF file that contains muliple sequences must be handled similarly to the .MSF file format, by following the filename with a {*} symbol, as shown in this example:

> PILEUP frag.rsf{*}

An .RSF file that contains a single sequence is more easily dealt with if you first REFORMAT it into a standard GCG sequence file:

	> netfetch af026976 

	NetFetch retrieves sequences from NCBI listed in a NetBLAST
	output file. You can also use it to retrieve sequences individually by sequence	
	name or accession number.  The output of NetFetch is an RSF file.

 	What should I call the RSF output file (* af026976.rsf *) ?

 NETFETCH complete with:

     Output: af026976.rsf
     Server: www.ncbi.nlm.nih.gov
  Requested: 1
   Returned: 1

	> reformat af026976.rsf{*} 

	Reformat rewrites sequence file(s), scoring matrix file(s), or
	enzyme data file(s) so that they can be read by GCG programs.

    	af026976.seq  length: 3113 bp

	> ls
	af026976.rsf  af026976.seq

Watch out for the syntax of the REFORMAT command. The {*} must follow the filename without a space. If you insert a space, GCG reformats the file into gibberish - turning the annotation into part of the sequence, and it deletes your original .RSF file, so you have to start over again with NETFETCH.

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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@mcrcr.med.nyu.edu