I tried ApE software, but there you can define just one ORF, I need to have intron sequence incorporated in the sequence. I want to avoid making it manually.
Hi Jaroslav, try in this website: http://rulai.cshl.org/tools/genefinder/
it was very usefull for me, although it's for human, mouse, arabidopsis or fission yeast, but, the result was identical to those predicted in Uniprot, for example, and I tried others web tool, and the only worked well was this.
Best regards.
Paul
Hi Jaroslav,
I am sure there is a single program that can produce your output, however, I can't recall where I saw it before. In the meantime, here are some close alternatives.
EMBOSS "showseq" creates a very similar output when "-format 4" is used: http://www.bioinformatics2.wsu.edu/cgi-bin/emboss.pl?_action=manual&_app=showseq
This website also provides a similar output: http://web.expasy.org/translate/
NCBI nuccore displays introns and exons in coding sequences, but in color.
EBI EMBOSS Sixpack translates DNA into six frames, some post-processing is needed to get the format above (may just be a simple grep call to eliminate unwanted lines): http://www.ebi.ac.uk/Tools/st/emboss_sixpack/
Use the Gene Construction Kit (GCK). You can download a demo version from the link below.
http://www.textco.com/gene-construction-kit.php
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