[Bioperl-l] ESTScan Query

[James Wasmuth]

Hi Sean

"tranalign" from the EMBOSS package will do what you ask...

word of warning about ESTScan there's a very small bug in the code that 
can severely affect your translations. In the main ESTScan script

replace
$pSeq =~ s/[acgt]//g; # Remove lowercases...

with
$pSeq =~ s/[acgtn]//g; # Remove lowercases...


james



Sean.Maceachern at dpi.vic.gov.au wrote:

>Hello,
>
>I am processing a number of EST sequences with ESTScan and was hoping
>someone could tell me if anything exists that can take an alignment from an
>ESTScan translation (protein) and align the corresponding nucleic coding
>regions maintaining the gaps etc... from the aligned protein.
>
>Any suggestions would be appreciated.
>
>Sean
>
>
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