[Bioperl-l] construct chromosome sequences from bac sequences

[Dan Bolser]

Did you try loading the sequences into an alignment or an assembly object?

As far as I know BioPerl won't call a consensus for you, but you can
post process the alignment or assembly to do that.

Can an alignment hold sequences with qualities?


Sorry for the late reply, I'm just trawling the list for potential
answers to the question I'm about to post ;-)

Dan.


2008/12/30 Alper Yilmaz <alperyilmaz at gmail.com>:
> Hi,
>
> I have FPC report and BAC sequences in hand. I was wondering what is the
> most practical way to build chromosomes from these available information.
>
> I HAVE:
> FPC file:
> accession    chr    chr_start    chr_end    contig    contig_start
> contig_end
> aaaaaaaaaa    1    14700    215600    ctg1    14700    215600
> bbbbbbbbbb    1    196000    362600    ctg1    196000    362600
> cccccccccc    1    352800    524300    ctg1    352800    524300
> .
> .
>
> BAC fasta file:
>>aaaaaaaaaa
> GATCGATCAGCATCGACTACGACT...
>>bbbbbbbbbb
> AGTAGCAGTAGCTAGCACTACGAC...
>>cccccccccc
> ACGATCAGCATCAGCATCGACTAC...
> .
> .
> .
>
> I WANT:
>>chr1
> GACGACTAGCTACGACTAC...
>>chr2
> AGCTGATCACGATCACGAC...
>
> In theory a sequence object called "Chr1" can be created and then according
> to start and end locations of each BAC in FPC file, subsequences of Chr1 can
> be retrieved. However, there are two facts which might prevent using
> standard sequence objects.
> 1) There will be gaps in chromosomes. Is there a function to convert
> unassigned locations to N?
> 2) There are overlaps between BAC sequences. If the overlapping sequences
> are exactly same, it won't be problem, but if there are discrepancies
> between them, a decision has to be made as to which sequence to use in final
> Chr1 sequence.
>
> thanks,
>
> Alper Yilmaz
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