gap4-aditionning sequences to an existing database

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu Sep 26 03:51:51 EST 1996

>Laureane wrote:
> Hi!!
> We have some problems using the gap4 program..and one of them is:
> We have tried to find in the program manuel how to add a sequence to a
> database that already exists, without success!...We have already put
> several sequences together to make a contig, but we now would like to add
> one or more sequences to it. If someone knows how to do it...

As Adrian Jenkins has already explained, simply use the normal shotgun
assembly routine again. We will try to clarify this in the manual.

> Something else we would like to do is to add a sequence that has not a
> chromatograph but only the text..

The solution here is simply to assemble the plain text sequences and forget
about chromatographs. The real issue is probably how to get the text files
into a form accessable by gap4. There are two possible routes.

1. If you don't wish to do any vector clipping, quality clipping or repeat
screening then simply produce a file of the plain text filenames (eg with "ls
*.txt > fofn") and give this name (fofn) to the shotgun assembly routine.

2. Use pregap. This can be used in an identical fashion for plain text files,
chromatagraphs, or experiment files, so there's a chance you've used this once
already. You'll still need to produce a file of filename as before, but with
pregap you get the option to mark vectors, clip poor quality readings, and
screen repeats. The file type you'll need to supply to pregap - the second
question asked I think - is "pln" (which somewhat cryptically stands for


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