R functions that extract the ORF from a sequence

Question

[peter.durr]

Hi everyone

I am working within R and need to extract the open reading frame (ORF) from a number of viral sequences

Somewhat to my surprise I have not yet been able to come across R functions within a package that find the ORF and readily extracts them.

Can anyone point me to R functions that will do these tasks?

Thanks

[Israel Barrantes]

Why in R? There are many other possible and straightforward solutions available (bedtools, EMBOSS, etc)

[peter.durr]

yes you are certinly correct - for sequence manipulation there are better tools

I am trying to do things in R because

1. of the downstream tools - especially for phylogenetics
2. I can code the total workflow into one replicable file

but.... in this case maybe R is not yet mature enough, and I will need to do the sequence manipulations outside of R and then work on a clean alignment for the analysis

[Joseph Pearson]

Are you attempting de novo prediction of all ORFs, or do you want to extract only the ORFs from known/annotated viruses?

[peter.durr]

I am extracting from known viruses - actually segments of influenza viruses

the challenge arises is when I download a lot of them from Genbank, the segments will be of variable lengths

the five starting scenarios are:

1. complete segment length (about 1741 nt for segment 4)
2. complete coding sequence (about 1704 nt for segment 4)
3. missing regions to the left - with no start codon
4. missing regions to the right - with no stop codon
5. missing left and right - no start and stop codon

I am hoping to develop a workflow that can classify the sequences in to the 5 groups - and I was hoping I could build on existing code

thanks

[Joseph Hughes]

This might be a good starting point:

http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter7.html

The SequinR package has a number of functions that deal with the prediction of reading frames:

https://cran.r-project.org/web/packages/seqinr/seqinr.pdf

Answer 1

[hauken_heyken]

The R package ORFik in Bioconductor has all you need, implemented in C++ and even takes circular genomes.