[Biojava-l] differences between read in sequence and stored sequence in database]

[Gabrielle Doan]

Hi all,
concering the problem as described below I have found out that this 
problem also occured in BioRuby and was fixed in 2004.
See: 
http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/lib/bio/db.rb?cvsroot=bioruby
Unfortunately I'm clueless about BioRuby. Does anybody recognize this 
problem or understand how it was solved in BioRuby?

I am grateful for any hints.

Cheers,

Gabrielle


-------- Original-Nachricht --------
Betreff: [Biojava-l] differences between read in sequence and stored 
sequence in database
Datum: Mon, 27 Oct 2008 13:57:03 +0100
Von: Gabrielle Doan <gabrielle_doan at gmx.net>
An: biojava-l at biojava.org

Hi all,

I have a BioSQL database which contains all human chromsomes. For my
recent project I have to query for a part of a sequence.
As far as I know I can get the whole sequence from the entry
Biosequence.Seq in the BioSQL schema. So I've made this query:

SELECT SUBSTRING(bs.seq, 131615042, 131626262) FROM biosequence bs;

But this query hasn't yield the desired string, because the length of
this biosequence is only 100,000,020 bp. I am very confused why I get
such a discrepancy. I have added all chromosomes with the build in
method in BioJava addRichSequence(RichSequence seq) to the database.
 From my raw data I know that this sequence should have a length of
140,279,252 bp. So where is the remaining part of my sequence? I have
observed these discrepancies on all chromsomes which are longer than
100,000,020 bp.

Here is an abstract of my database:
bioentry_id	description	length	
2	Homo sapiens mitochondrion, complete genome.	16571	
3	Homo sapiens chromosome Y, reference assembly, complete sequence.
57772954	
4	Homo sapiens chromosome X, reference assembly, complete sequence.
100000020	
5	Homo sapiens chromosome 22, reference assembly, complete sequence.
49691432	
6	Homo sapiens chromosome 21, reference assembly, complete sequence.
46944323	
7	Homo sapiens chromosome 20, reference assembly, complete sequence.
25960004	
8	Homo sapiens chromosome 9, reference assembly, complete sequence.
100000020	
9	Homo sapiens chromosome 7, reference assembly, complete sequence.
100000020	

Sequences smaller than 100,000,020 bp are correctly stored under
Biosequence.seq.

I am grateful for any hints, which explain the behaviour of my database.

Cheers,

Gabrielle
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