Annotating Sites in Sequence Files ??

Peter Rice pmr at unst.sanger.ac.uk
Tue Jan 24 08:21:45 EST 1995

In article <D2vA2B.Cv9 at rockyd.rockefeller.edu> myersm at rockyj.rockefeller.edu (Michael Myers) writes:
> It would help immensely if I could at least
> mark the positions of primers that I have designed in the GCG file
> itself. Is the only way to achieve this using the Comment feature of
> SeqEd? I haven't tried it, but from pictures in the manual it seems that
> this actually disrupts the sequence when viewed. Also, are the comments
> retained when using Map? I know I can just put the primer sequences in
> the Header, but it would be nice if the nucleotides in the sequence
> display were marked in some fashion. I also have primers for the opposite
> strand, and I don't see how Comment would help there.

> I have checked all the features and optional parameters for Map, SeqEd,
> and Publish, but couldn't find anything to fit the bill. Have I missed
> something or has anyone devised a kludge to get this?

> In its best implementation, it would work something like the -MARK
> parameter in MapPlot. A table of primer sequences and their given names
> in the SeqEd file itself, that is referenced each time the file is
> utilized.

As it happens, this is included in EGCG's GelPicture. This program displays
a contig as a text file, with the fragment numbers matching those in
GelAssemble. You keep a file with the primer sequences in the pattern
format used by MapPlot, Map and Findpatterns. The primers are displayed
below the contig.

There are some limitations, one being the need for a perfect match
to the primer so any temorary gap in the consensus will destroy the match
and another being that EGCG 8.0 is not yet ready (but will be out soon).

You can also use such a pattern file in MapPlot, Map or FindPatterns to
report the primer locations. You can also use them to find restriction
sites, known exon sequences, and so on.

As for comments, I too would like them in the fragment files but they would
not be preserved at present when a fragment or a contig is updated.

GCG's Fragment Assembly, once the method of choice (well, I chose it once :-)
is now looking sadly dated compared to, for example, the changes in the Staden
programs. With some work it could catch up, and the changes would be useful
in other GCG prorams too. If only ...
Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr    | England

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