GelAssemble problem

Francois Jeanmougin pingouin at crystal.u-strasbg.fr
Wed Aug 7 05:21:28 EST 1996

In article <4u87rc$gle at wiscnews.wiscnet.net>,
	kpleyte at post.its.mcw.edu (Kay A. Pleyte) writes:
>     I'm trying to assemble a group of overlapping fragments with
>GelMerge/GelAssemble but it's not recognizing any overlaps.  I entered eleven
>fragments, and the only output I get is eleven separate contigs. 
>     Should I be entering a consensus sequence before I enter the
>fragments?  If so, how do I do that?  
>     I must be missing something.  If someone could point me in the right
>direction I would appreciate it.
>Kay Pleyte
>kpleyte at post.its.mcw.edu

	Well, you should have miss something, that is the definition of
an overlap for gelmerge. That is that the overlap must be at an extremity
and not in the middle of the sequence. Don't flame, it's an evidence, I know
But now you have to be sure that the ends of the sequences are clean.
	If you are using sequences from automated sequencer, I've made
a tool (SeqCleaner) for the GCG environment that check quality and 
removes ends with to many N's. It also look for vector, but there is
a bug at this part (I'm working around...).
	If you are using cleaned sequences, It should work...
Try doing a fasta or run overlap between all the sequences, then
look carefully at the output, it will tell you if the ends are clean.

						Hope theis helps.


Francois Jeanmougin
Service de bioinformatique / bioinformatics service
BP 163 
67404 Illkirch France
tel : (33) 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr

Nagasaki ne profite jamais (STTELLLA)

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