Could this be a database implementation issue? Is there a limit on how long a field can be in your DB?
- Mark On Mon, Oct 27, 2008 at 8:57 PM, Gabrielle Doan <[EMAIL PROTECTED]> wrote: > > 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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
