handling ESt

Danielle et jean Thierry-Mieg mieg at BETA.CRBM.CNRS-MOP.FR
Tue Jun 29 07:55:43 EST 1999


I am sorry to interfere on the staden bionet to talk of a
different software, apologies to Roger and James in particular, but 
i wish to say that acembly est is dedicated to assemble EST on
genomic sequence and works very well on C.elegans
the input essentially is 2 fasta files
1) the genomic sequence
2) the ESTs
in addition it is better toi provide the assembly of the genomic cosmids
because many genes overlap on 2 neighbouring cosmids or bacs
and the info on cdna is 2 or more est come from the same cdna
i.e. a 3prime and a 5prime read and of course the sequencing vector
and the size of the cdna clones if available

please mail mieg at crbm.cnrs-mop.fr for details
acembly est works well on the whole C.e.: 100Megabase genomic, 100.000 est
all in one go



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