Handling EST sequences

Felipe Rodrigues da Silva felipes at TURING.UNICAMP.BR
Mon Jun 28 15:43:39 EST 1999


We are just starting an EST project (sugar-cane). Despite the fact that
I do think Staden is far much more complete than phred/phrap/consed (and
I have a personal bias in loving the former), the solution found to
manage data here was to use the latter (phred/phrap) to analyze and
generate the fasta files we need. All requirements proposed in your
message are done by scripts that call components of phred/phrap.

     I would be very interested in hearing from anyone using Staden in
EST projects.

		Felipe.

"l. heijnen" wrote:
> 
> Hi,
> 
> We are currently evaluating software packages that are able to analyse short
> (<500 bp)EST sequences in a high-trougput, automated mode.
> 
> We are determining the EST sequences on an ABI 377.
> We would like to have base calls with quality scores.
> Vector sequences should be trimmed off automatically.
> Some (basic) assembly should be possible (forward/reverse run).
> Editting should be possible on trace files.
> Output sequences should be in Fasta format.
> The complete process should be fast (with very little "hands on work")
> 
> Would the Staden package be a good choice to handle this job?
> Are there any other suggestions?
> 
> Thanks
> 
> L.heijnen at hccnet.nl

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