[Bio-software] Re: GCG non-support
(by pmr from ebi.ac.uk)
Fri Aug 3 16:55:10 EST 2007
Steve Thompson wrote:
>> Can you make a quick list of the additional functionality you would
>> like to see [in GDE]? I seem to recall "rich sequence format" was one
>> of GCG's major extensions.
> Yes, some have already been mentioned in this thread; I think these two
> are the most important:
> 1) The ability to directly load sequence data from output sequence lists
> from other programs such as BLAST, FastA, and a reference searching
> program (in GCG that is the SRS derivative LookUp) with the option of
> trimming that data to the length id'ed by a similarity search. As Nick
> mentioned this ability to handle "ad-hoc" databases can be very powerful.
That input should be simple (something like EMBL:X13776) and the code is
relatively easy to do
> 2) The ability to display FEATURE information from database entries in
> colored and graphical representations. This is especially helpful for
> homology inference of active sites and secondary structure.
That was the part that used "rich sequence format" to store rearranged
features and markup.
I expect it can be reproduced using GFF as the feature standard (EMBOSS
uses GFF internally, it is a good fit with even the EMBL/Genbank/DDBJ
feature table and extendable for colouring etc - Artemis does something
> Too bad, but I'm glad there are alternatives. Perhaps some variation of
> NCBI's stand alone Entrez, but it is designed for ASN.1 data . . . . .
Or MRS from CMBI in Nijmegen. Or something using web services. There are
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