Kym,
You sent the below to acedb at sanger.ac.uk which reaches the acedb developers but
probably your note is more appropriate to the acedb newsgroup as it covers a
topic which is of concern to many. I have taken the liberty of copying this to
the newsgroup.
cheers Ed
On Tue, 15 Jan 2002, Kym Hallsworth-Pepin wrote:
> Hello,
> On the acedb.org web site (below) I read about a discussion
> to allow a dump of a superlink sequence file with known
> mismatches ,but it wasn't resolved as to how
> this could be done. Is there away to dump
> a sequence file, which has mismatches, to one
> contiguous file i.e. no dashes?
>> thanks
> Kym
>> Folks got a bit distracted here discussing the issue of actually forming the reference sequence. If you have
> two sequence with different bases at a mismatch-position, which one should dominate? Should any
> quality-values be attached to the mismatches and ACeDB follow some procedure to decide on the final
> ref-sequcence? Or should it remain as it has, and only display what it is given and have an external
> program do the actual refseq-building?
> It is obvious that there are different opinion on this subject, with Richard D. firmly in favour of the more
> 'static' approach of displaying the data, and folks like Lincoln in favour of a more complex system of
> high/medium/low quality values for the mismatches. We'll see what happens.
>
--
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| Ed Griffiths, Acedb development, Informatics Group, |
| Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, |
| Hinxton, Cambridge CB10 1SA, UK |
| |
| email: edgrif at sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 |
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