Menu
▾
▴
Re: [SO-devel] Matches and match parts
|
From: Karen E. <kei...@ge...> - 2007-04-11 18:06:03
|
Hi all, I will obsolete the term match_set from SO and SOFA as agreed in discussion below. Cheers, Karen On Apr 4, 2007, at 2:34 PM, Lincoln Stein wrote: > Hi Sofia, > > Well, you use "protein_match" for the first one, and > "translated_nucleotide_match" for the second one. Also, the first > one uses nucleotide coordinates and the second uses protein > coordinates. > > Best, > > Lincoln > > On 4/4/07, Sofia Robb <so...@ne...> wrote: > Hi Lincoln, > > Makes sense to me. > > I have a question, it applies to my current use of match_set and > protein_match / nucleotide_match and your new proposal. > > what do you do for > > protein query against nucleotide db > nucleotide query against protein db > > Sofia > > > > > On Apr 4, 2007, at 9:17 AM, Lincoln Stein wrote: > >> Hi Sofia, >> >> What you're doing is what you have to do with the current SO, but >> it isn't ideal. One has to examine the subfeatures in order to >> determine the nature of a hit (nucleotide=>nucleotide, >> protein=>nucleotide, etc). Under the new proposal, the match would >> be typed (nucleotide_match), and the match_part would be generic. >> How does this sound to you? >> >> Lincoln >> >> On 4/2/07, Sofia Robb < so...@ne...> wrote: >> 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 >> >> >> >> -- >> 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... > > > > > -- > 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... > ---------------------------------------------------------------------- > --- > 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 |
