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
"l. heijnen" wrote:
> 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?
> L.heijnen at hccnet.nl
Felipe Rodrigues da Silva | phone: (+55-19)788-1144
CBMEG - UNICAMP | fax: (+55-19)788-1089
CxP 6109 CEP 13.083-970 | __o
Campinas - SP Brazil | _ \<,_
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