MICPRF@latvax8.lat.oz (07/09/90)
I am not sure if this news group takes questions but here goes - Can the nucleic acid data bank be used to search for homologous sequences at the protein sequence level and not just the nucleotide sequence level? Is this publicly accessible in the way that searches at the nucleotide sequence level are? Thanks. Paul Fisher (micprf@latvax8.lat.oz.au).
dadler@blake.acs.washington.edu (David Adler) (07/10/90)
Hi, Your question: YES - TFASTA will take a query amino acid sequence and translate Genbank DNA entries into 3 reading frames and score alignments. It's neat and it's free - written by Pearson and Lipman. Files are available via anonymous ftp from ??.virginia.edu Contact Bill Pearson wrp@virginia.EDU wrp@virginia.BITNET ...!uunet!virginia!wrp for details -- David A. Adler University of Washington Pathology SM-30 Seattle, WA 98195
kristoff@genbank.BIO.NET (David Kristofferson) (07/13/90)
Paul, We have two programs on the GenBank On-line Service (GOS) which can compare a protein sequence against the translated nucleic acid sequence databank. One is TFASTA as mentioned in one reply to your message and another possibility is the IntelliGenetics program FASTDB which will translate the nucleic acid sequence databanks in up to six frames during the search. Both of these programs are available on GOS, but only to interactive users of the system (not by e-mail). The GenPept database is available free of charge from genbank.bio.net by anonymous FTP. That databank contains translation of all annotated coding regions in GenBank. Also note that GenPept and the GenBank and EMBL databases are updated daily with the latest sequence data. -- Sincerely, Dave Kristofferson GenBank On-line Service Manager kristoff@genbank.bio.net
MICPRF@latvax8.lat.oz (07/20/90)
In article <532@latvax8.lat.oz>, I (MICPRF@latvax8.lat.oz) wrote: > I am not sure if this news group takes questions but here goes - > Can the nucleic acid data bank be used to search for homologous sequences > at the protein sequence level and not just the nucleotide sequence level? > Is this publicly accessible in the way that searches at the nucleotide > sequence level are? Thanks. Paul Fisher (micprf@latvax8.lat.oz.au). > This is a note to thank publicly the several people who responded to my query. The responses here cover it fairly well, but Bill Pearson was kind enough to email me more detailed info. I would be happy to send this on to anyone who may be interested, to save Bill the trouble. (Bill, I assume you don't mind). Thanks, Paul Fisher.