Question: how to convert Locus tag to old locus tag?
1
gravatar for Paul
5 months ago by
Paul50
India
Paul50 wrote:

I have a few new Locus tags as follows:

RS09560
RS10020
RS10595

and I need to convert them into old Locus tag which are

RS09560     NA
RS10020     1984
RS10595     2097

NA are the ones with not available old locus tag. I couldn't find any database to do so. And the information available for old locus tag and new locus tag is in the NCBI website

https://www.ncbi.nlm.nih.gov/nuccore/NC_000962.3

I tried to scarp the data from the website using R (rvest) and had written a few lines, but skeptical about the HTML node I should extract from the web page to get the information about old locus tag and new locus tag.

> library(xml2)
> library(rvest)
> url <- 'https://www.ncbi.nlm.nih.gov/nuccore/NC_000962.3'
> webpage <- read_html(url)
> sb_table <- html_nodes(webpage, ' ')

Please suggest a way to do and also which node could be used to fetch the locus tags.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Paul50
1
gravatar for Jenez
5 months ago by
Jenez470
Sweden
Jenez470 wrote:

I'm a python type of guy, and what I would do is to set up a script to parse through the genbank file using biopython.

I wouldn't expect to find any source that has any old locus names that are missing from the NCBI genbank files. Gene annotations are constantly updated and it's not unusual for 'novel' genes to pop up, which will not have an old locus name.

Assuming that what you have is a neat list of accessions of interest, it is just a matter of looping through the 'Features' and looking for the accessions, grabbing the old locus names if available, and print a simple list of new vs old accessions.

Even if you have not touched python yet, it is a fairly easy and decent introduction to it if you are willing to give it a go.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jenez470
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1469 users visited in the last hour