Path: utzoo!utgpu!news-server.csri.toronto.edu!bonnie.concordia.ca!uunet!stanford.edu!agate!bionet!lhc!ncifcrf!fcs260c2!toms From: toms@fcs260c2.ncifcrf.gov (Tom Schneider) Newsgroups: bionet.molbio.genbank Subject: Re: Software for automated subseqence extraction Message-ID: <2140@fcs280s.ncifcrf.gov> Date: 1 May 91 13:53:17 GMT References: Sender: news@ncifcrf.gov Organization: NCI Supercomputer Facility, Frederick, MD Lines: 27 In article kristoff@GENBANK.BIO.NET (Dave Kristofferson) writes: >> I am looking for some software that will allow me to extract subsequences >> from genbank or PIR. >> For example, I would like to be able to provide a keyword such as 'splice >> site' and have the program search genbank and return with a list of sequence >> names and the subsequence from each entry corresponding to my keyword. >The most expeditious way of doing this is through the free GenBank IRX >account. Instructions are included in the information below. This person wanted PARTS of genbank entries, not whole entries! Since GenBank entries do not carry a coordinate system with them, it is not possible to extract subsequences without losing the location of the sequences. One must add a new feature to the entries: a coordinate system. Do you understand the situation Dave? Genbank does not serve the needs of this user. He needs software that can manipulate portions of entries. > Dave Kristofferson > GenBank Manager > kristoff@genbank.bio.net Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov