[Bioperl-l] CONTIG sequence files from the NCBI

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Feb 16 05:31:54 EST 2006


Hi

I have two questions really.  I fetched bacterial genome sequences from
the NCBI using Bio::DB::GenBank.

Some of these sequence entries are CONTIG sequences, ie they just point
to other sequences that need to be joined together to form the entire
genome.

Looking at my downloads, it looks as if bioperl has done all the
necessary joining for me - or maybe it was the NCBI that did the
joining?

OK, so firstly, did bioperl do the joining, and if so, are all the
co-ordinates of the features updated to reflect their new location on
the new, joined sequence?

And secondly, sequence versions... I'm thinking that possibly the
sequence version of the CONTIG may be 1 (as it hasn't changed) yet the
versions of the sequences it refers to might have changed, so when I ask
bioperl if these sequences have been updated, I will be told no because
the CONTIG sequence version is 1, but I should be told yes because the
underlying sequences have...?

Make sense?

Thanks
Mick



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