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Re: [SO-devel] Matches and match parts
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From: Sofia R. <so...@ne...> - 2007-04-02 17:05:50
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Hello All, i usually use match_set to represent the HIT and nucleotide_match or protein_match to represent the HSPs. sofia On Mar 29, 2007, at 2:31 AM, Richard Durbin wrote: > Karen and Lincoln's proposed solution sounds sensible and good to me. > > Richard > > Lincoln Stein wrote: >> Hi Karen, >> >> That was the solution I was hoping for. Can it be done? >> >> Lincoln >> >> On 3/28/07, *Karen Eilbeck* < kei...@ge... >> <mailto:kei...@ge...>> wrote: >> >> Hi Lincoln, >> Sorry for the delay getting back to you. I'm at a Dagstuhl at >> meeting. >> >> I think this has always been confusing and now that I look at it, >> I don't think it works as advertised. >> I think it would make logical sense if we removed match_set and >> had match_part (HSP) be part of a match. >> Then any kind of match such as EST_match could have a match_part >> But that might be too easy. >> >> -K >> >> On Mar 28, 2007, at 9:38 AM, Lincoln Stein wrote: >> >>> Hi, >>> >>> I'm trying to figure out how to represent HSPs that are part >>> of a >>> larger match. The relevant section of the DAG is enclosed, >>> and it >>> shows that "match_part" is part of "match_set" and that >>> match_set >>> ISA match. Meanwhile, expressed_sequence_match also ISA match. I >>> would like to assert that an HSP is a match_part which is then >>> PARTOF an expressed_sequence_match, but I'm not sure whether the >>> traversal rules allow this. Can anyone comment? >>> >>> Lincoln >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT mic...@cs... >>> <mailto:mic...@cs...> >>> <match_question.gif> >> >> >> >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> FOR URGENT MESSAGES & SCHEDULING, >> PLEASE CONTACT MY ASSISTANT, >> SANDRA MICHELSEN, AT mic...@cs... <mailto:mic...@cs...> >> --------------------------------------------------------------------- >> --- >> >> --------------------------------------------------------------------- >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> --------------------------------------------------------------------- >> --- >> >> _______________________________________________ >> SOng-devel mailing list >> SOn...@li... >> https://lists.sourceforge.net/lists/listinfo/song-devel >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > SOng-devel mailing list > SOn...@li... > https://lists.sourceforge.net/lists/listinfo/song-devel |
