Annotating Sites in Sequence Files ??

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Tue Jan 24 06:46:42 EST 1995

In article <D2vA2B.Cv9 at rockyd.rockefeller.edu> myersm at rockyj.rockefeller.edu (Michael Myers) writes:
>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

While I haven't used the GCG software for fragment assembly, Staden's sequence
assembly software handles these problems well.  It is very simple to tag
regions within sequences with comments of various categories (user definable)
and with the new assembly program, (x)gap, even the consensus sequence, too.

I would be most interested to hear what GCG can do in this respect.



>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
>I am in the learning stages of using the Fragment Assembly System. Any
>warnings or suggestions would also be welcome.
>Michael Myers
>myersm at rockvax.rockefeller.edu 

Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
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