From owner-celegans@net.bio.net Sun Aug 11 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!news.new-york.net!news.columbia.edu!chalfie-mac.bio.columbia.edu!user From: schwarz@cubsps.bio.columbia.edu (Erich Schwarz) Newsgroups: bionet.celegans Subject: Genefinder for the Masses -- Possibility or Hopeless Dream? Date: Mon, 12 Aug 1996 05:09:57 -0400 Organization: Dept. of Biol. Sci., Columbia Univ. Lines: 23 Message-ID: NNTP-Posting-Host: chalfie-mac.bio.columbia.edu X-Newsreader: Yet Another NewsWatcher 2.1.8 I've been trying to get BLAST data from a partially sequenced cosmid that's of interest to our lab, and I've been forced to the following realization: The public BLAST servers *really* don't like you if you try to search reasonably sized chunks of DNA. I got NCBI to search 9 kb exactly once, but it took God's own time, and the output got yanked away between when I saw it came up and when I would have been able to download it. Fooey on that. So. Does anybody out there know if there's either a publicly available server or a transferrable version of _C. elegans_ Genefinder that we could use here at Columbia on cosmid sequences? If there was just a way to distill 40 kb of DNA to a few possible proteins, BLAST searching the residue would be a joy. Thank you for any advice. I'm sure there's an obvious answer, but this seems to be my day to be computer illiterate. --Erich Schwarz schwarz@cubsps.bio.columbia.edu .