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NCBI ORF Finder Problem

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NCBI ORF Finder Problem

Postby cnite » Sun May 11, 2008 12:35 am

Hello, all!

Question #1:

I don't understand how to make NCBI ORF Finder to react on another than ATG start codon.
I set Table 11 (Bacterial code) (http://www.ncbi.nlm.nih.gov/Taxonomy/Ut ... ode=t#SG11)
and feed it with FASTA code of MS2 bacteriophage (http://www.ncbi.nlm.nih.gov/entrez/view ... gin&to=end) This phage has ORF on position 135 starting
with GUG. In the Table 11 this codon is checked with "i" i.e. Orf has to be aware of it, but results do not see it.

What to do?

Question #2:

I want a sequence analyser tool that will parse FASTA code fully, i mean that it will find ORFs, RBSes, TATA-boxes, not only ORFs. Is there such tool you can advise?

Thanks
cnite
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Postby mith » Sun May 11, 2008 6:01 am

There's a graphical interface one
http://www.biology.utah.edu/jorgensen/wayned/ape/

You can set your own features
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Postby cnite » Sun May 11, 2008 3:58 pm

Thanks.
It's cool, but still I don't see how to make it recognize other start codons than atg...
cnite
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