dumping without mismatches

Ed Griffiths edgrif at sanger.ac.uk
Thu Jan 24 06:09:45 EST 2002


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.

| 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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