Question: NCBI ORFfinder - How Does It Work
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gravatar for A Soggy Waffle
7 days ago by
A Soggy Waffle0 wrote:

NCBI help desk hasn't been very helpful to me on this so far.

I'm looking for any record or docs on the ORFfinder tool. I want to know how it finds ORFs. Not how to use it, but how it determines what is and is not an ORF. Is it regex, HMM, fairy dust? Maybe such docs are posted somewhere but I can't seem to find them.

Thanks

ncbi • 92 views
ADD COMMENTlink modified 7 days ago by h.mon25k • written 7 days ago by A Soggy Waffle0
1

Video above contains an email address of a person who probably still supports this tool. You can try writing to them directly. It does not contain the information you are looking for.

Note 1: ORFfinder is not meant to be a gene prediction tool for eukaryotes.
Note 2: NCBI help desk can take up to 3 working days to respond. Likely because of volume of queries they get. I have always received an answer for my questions.

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax67k

Download the program from here. gunzip it and add execute permissions chmod a+x ORFfinder. Run it to look at in-line help.

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax67k

I guess I wasn't clear enough. It's not the arguments and calling the program that's the problem. I want to know how it finds ORFs, algorithmically.

ADD REPLYlink written 7 days ago by A Soggy Waffle0

See my note below.

ADD REPLYlink written 7 days ago by genomax67k

If this is the ORF finder I think it is, I don’t think it’s much more sophisticated than finding start and stop codons in all 3 frames on each strand, and highlighting the interval as a potential ORF. Possibly some filtering for minimal sizes.

‘Proper’ gene predictors like Prodigal and Glimmer have much more sophisticated characteristics like sequence complexity, homology, etc.

ADD REPLYlink modified 7 days ago • written 7 days ago by jrj.healey12k
0
gravatar for h.mon
7 days ago by
h.mon25k
Brazil
h.mon25k wrote:

ORF Finder perform six-frame translation of a nucleotide sequence given a particular genetic code, finding all ORFs possible. It then filters for ORFs above a certain size threshold, and may exclude ORFs nested inside longer ORFs. This information (and nothing more) can be found at the paper Database resources of the National Center for Biotechnology.

ADD COMMENTlink written 7 days ago by h.mon25k
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