[BiO BB] sequence retrieval

Sameer_Mohta Sameer_Mohta at satyam.com
Tue Feb 19 01:40:37 EST 2002


i have a small query regarding BIoDAS.As Haibo Zhang asked about retreiving
information of a particular gene, and you suggested that BioDAS can serve
the purpose. But my question is that BioDAS server has to be up on the
specified server for that. or is it possible to reteive information without
BioDAS server. b'coz as far as my knowledge is concerned, BioDAS is running
on TIGR, Ensembl, Flybase and 2-3 other sites.


-----Original Message-----
From: Roger Pettett [mailto:rmp at sanger.ac.uk]
Sent: Monday, February 04, 2002 12:54 AM
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] sequence retrieval

Have you looked at BioDAS? It sounds like you're duplicating effort as I'm 
pretty certain DAS does most of this for you. Check http://biodas.org/

Hope it helps,

On Sun, 3 Feb 2002 hz5 at njit.edu wrote:

> Hi group,
> I wrote a tool in java in order to retrieve any region of a gene from
> genome draft sequence.
> The tool is like, say, I want -200 to +100 sequence of gene FUBP3(Genbank
> is U69127), and the 300bp sequence will be retrieved.(upstream 200 and
> downstream 100)
> I also implement batch retrieve. The way I parse and retrieve is simply
make a
> socket connection to NCBI and parse the webpage to get information, pages
> tools involved are UniGene, LocusLink, and ASN.1 file.
> Questions and problems:
> 1. is there any biojave tool I can use here to make my tool compatible to
> biojava. I mean, I want to use biojava api to replace the same function in
> code, because it is always a good idea to keep with the common source.
> 2. I am using contig to address the upstream and downstream sequences
> this raise a problem when a gene is located at either end of the contig, I
> cannot find where is the information to tell what is the ajacent contig to
> one. Say if a gene begins at position 20 on contig NT_001100, if I want
> 200, I couldn't get it from this contig, I must know the contig that is
> with this and retrive the sequence accordingly. But I currently don't know
> this information is at NCBI.
> 3. I found that the contig that NCBI used for LocusLink is different in
> contig they depict in the human genomic project draft report, any thought?
> 4. my class can also count atgcn composition and build random sequence
> to the compostion; also can build first layer markov chain and build
> sequence accordingly(tends to keep dimer composition). I used java
> Math.random(),  is it safe? Are these tools already been implemented in
> or they can be of some help?
> Any evaluation and suggestion are highly appreciated! Thanks!
> Haibo Zhang
> _______________________________________________
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 Roger Michael Pettett             Email: rmp at sanger.ac.uk
 Project Leader (Web Systems),     Web: http://www.sanger.ac.uk/
 The Sanger Institute
 Wellcome Trust Genome Campus
 Cambridge CB10 1SA

BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
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