Re: [SO-devel] Matches and match parts

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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...>
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>
> --
> 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...