gap4-aditionning sequences to an existing database

Adrian Jenkins ajenkins at
Thu Sep 26 02:06:05 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...
> Something else we would like to do is to add a sequence that has not a
> chromatograph but only the text..
> THANK YOU for helping us!!

I have a method which works, but im not sure whether it is the
'officail' approach..

The way i do it is very similar to starting a contig database.

1-  if necessary convert your sequence files into staden format.

2-  create a list of file names using the unix ls and pipe commnads.

3-  start gap4, and open up existing database.

4-  go to assembly ands select 'normal shotgun assembly' and fill in
the  blanks on the form.

5- click on okay and hopefully the sequences are added to the existing

Does this answer your query??




        (A W.H.O. International Laboratory for Standards)

	Adrian Jenkins
	Aids Collaborating Centre		    Blanche Lane,
        e-mail Work ajenkins at  	    South Mimms
               Home ajenkins at   Potters Bar     
        voice      01707 654753 X 439		    Hertfordshire
        fax        01707 649865			    England EN6 3QG                    
          "No plan survives contact with the enemy"  von Moltke


More information about the Staden mailing list