Suggestions for SRS use w/ nonsequence gene data
pmr at sanger.ac.uk
Thu Aug 17 09:13:28 EST 1995
In article <40vfeu$jb3 at usenet.ucs.indiana.edu> gilbertd at sunflower.bio.indiana.edu (Don Gilbert) writes:
> Here are some suggestions for SRS that have arisen from trying to use
> it with Drosophila genome data:
> 1) indexer interface: needs to permit indexing of any character/symbol set.
> Drosophila genes use just about the full ASCII printable symbol set
> (and would use more if possible).
One for Thure, but I suspect your wish (and mine) will soon be granted :-)
> 2) query interface: needs to permit any character/symbol set to be valid
> data in the query, and query symbols should be configurable.
> Use of words instead of symbols as query operators
> should be optional at least, and by my preference they would be default.
I would be happy to just have escaping of critical characters like \(\)\&\|
but certainly something is needed.
> 3) output interface: needs to allow addition of post-processor functions
> to convert data to various human-usable formats. This is done now in
> part for sequence data and for adding html links, but not in a
> general way that would allow addition output formatting per database
> w/o rewriting the basic SRS code.
> Here is roughly how I did it for flybase data, but it is a hack
> not a general solution. Example outputs show this formatted output
> from iubio server, versus the computer "star code" output from the
> sanger server.
This looks a really neat idea !!
Not only is it nice in the flybase cases, but it could also save me the
problem of converting many tab-delimited databases with perl scripts
into something with readable "entries" that I can parse and display.
Of course, first I need a parser that can handle tab-delimited databases :-)
On a related note, I would like to be able to put some extra text on the
">" line of FASTA format output - with the aim of using SRS to generate a
database subset for blast indexing and searching. Then (for example) the
accession number and definition could appear in the blast search results.
Peter Rice | Informatics Division
E-mail: pmr at sanger.ac.uk | The Sanger Centre
Tel: (44) 1223 494967 | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919 | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/ | England
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