[Bio-software] Re: GCG non-support

Peter Rice via bio-soft%40net.bio.net (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 
similar)

> 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 
  many possibilities.

Peter



More information about the Bio-soft mailing list