IUBio

Annotating Sites in Sequence Files ??

Michael Myers myersm at rockyj.rockefeller.edu
Mon Jan 23 11:34:58 EST 1995


I am in the process of doing a lot of sequencing and contig assembly. One
nightmarish aspect of this project that I have realized is maintaining
up-to-date sequence files. This includes assembling the overlaps and
correcting small sequence ambiguities. Early in the process, I prepare
Maps of each sequence to locate restriction sites and assist in
designing new primers.  I ultimately print out new versions as contigs
are generated and errors corrected, but these new print-outs lack all the
"pencilled in" information. 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.

I am in the learning stages of using the Fragment Assembly System. Any
warnings or suggestions would also be welcome.

Thanks, 

Michael Myers
myersm at rockvax.rockefeller.edu 



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