Finding Distance Between Genes On Same Chromosome

Question

[Divya]

Hi I'm new to genomics I'm doing project in (GATA)n repeats of rice I have found out the genes in which these repeats are present

Now how can I find the distance between these genes??

Thanks in advance

Thanking you, Divya

[Michael]

distance in what sense? genomic distance? or maybe similarity of the AA sequence??

[Michael Schubert]

I agree with Michael, you first need to know which kind of distance you want to calculate. Just some examples: Hamming distance, 1/alignment_score, maybe even the number of repeats in your case. Note that there are more sophisticated methods, which one you want to use may well vary.

Answer 1

[brentp]

If you have a list of genes, you can use phytozome's biomart which has Oryza Sativa ( www.phytozome.net/biomart/martview ) from there, you'll do:

1. Choose Dataset: Phytozome 6 Genomes
2. Click Filters on the left then choose "Oryza Sativa" on the right for organism.
3. Click the [+] box next to "GENE" and past your gene list in the box
4. Click "Attributes" on the left, then choose "Gene Start" and "Gene End" on the right.
5. Click "Results" at the top. From there you can change the output to CSV, import into excel or your tool of choice and easily calculate distances.

To automate this, you can click the "Perl" button at the top which will output much of the perl code necessary to access biomart programatically. Likewise, you can make a request by POST'ing XML from the "XML" button.

Answer 2

[Larry_Parnell]

In many cases, for a plant like rice (important crop, model for grasses), the distance of interest is genetic - how many cM (centi-Morgans) between genes containing the repeat of interest. Links within here will lead to you the genetic marker data and affiliated maps.

Yes, the question was a little vague, but perhaps the instructions to Divya were also vague. This is then an example where bioinformatics and research colleagues need to have longer, more detailed conversations before the project/assignment starts.