[BiO BB] sequence retrieval

Roger Pettett rmp at sanger.ac.uk
Sun Feb 3 14:23:44 EST 2002

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 human
> genome draft sequence.
> The tool is like, say, I want -200 to +100 sequence of gene FUBP3(Genbank AccID
> 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 and
> 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 my
> 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 positions,
> 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 this
> one. Say if a gene begins at position 20 on contig NT_001100, if I want upstream
> 200, I couldn't get it from this contig, I must know the contig that is overlap
> with this and retrive the sequence accordingly. But I currently don't know where
> this information is at NCBI.
> 3. I found that the contig that NCBI used for LocusLink is different in the
> contig they depict in the human genomic project draft report, any thought?
> 4. my class can also count atgcn composition and build random sequence according
> to the compostion; also can build first layer markov chain and build random
> sequence accordingly(tends to keep dimer composition). I used java
> Math.random(),  is it safe? Are these tools already been implemented in biojava
> 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

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