How to convert bacterial gene id to another form?

Question

[doglip1987]

Hi, I am working on bacterial RNA-seq and just got the result from the sequencing company. I received the differential gene expression result and now want to proceed to GO and KEGG pathway analysis.

The problem I am facing is that, the gene identifier on the result is ncbi locus tag (ex. NT01EI_0934). I tried several different programs but none of them can recognize this form of identifier. Also I tried DAVID and few other gene conversion tool but they did not provide service for my organism.

Can anyone help me to solve this problem? FYI, my organism of interest is Edwardsiella ictaluri.

I am pretty naive to bioinformatics so web-based or windows-based tools will be better for me to understand.

Thank you in advance,

Julie

Answer 1

[Jenez]

If you go to NCBI and simply search using the term NT01EI_0934, you will find this gene entry.

You see here that the locus tag differs from the one you have. That's because you have yielded the 'old locus tag' from the sequencing centre. Whether this makes a difference I do not know, but it might be worth a shot. There are other bits of information further down on the page that might be of help as well.

Additionally, if it is a completely different name you are looking to find, say a common name, I would advice that you run a simple blastx search against NCBI's nt dataset and see if any of the results presents an optional name.

Hopefully this was of some assistance. Good luck.

[doglip1987]

Thank you for helpful comment, Jenez.

By the way, what I understand from your comment is that I need to check and update the locus tag to newer one or another alternative name manually one by one. I would like to leave this method last because I have hundreds of differentially expressed genes for pathways and GO analysis. Is there any way to run this automatically?

Thank you again !

[Jenez]

To be honest with you GO terms and the like is not something I have a lot of expertise of. Someone can probably help you out better than I, but if you specify what exactly it is you want to achieve with the name I might be able to point you in the right direction in terms of automation. It's all a matter of what you want to achieve and where to find the relevant information.

Getting the new locus name from the old locus name is very easy, but again, it depends on what you actually intend to achieve downstream.

[doglip1987]

I think if I can convert this old locus tag to another gene identifier (ensemble, entrez, or even gene symbol etc), then I can proceed downstream analysis of GO and KEGG pathway using DAVID tool or some other programs.

So can you explain the way to convert?

Thanks a lot for your kind comment so far!