SOL-GENOMICS: Find in which gene a specific region belongs to.

Question

[arronar]

Hi

As title says, I am trying to find in which gene a specific region belongs to.

I'm using solgenomics and for example I'm trying to find in which gene is the region 733456.

So in Landmark or Region: field I put SL2.40:723456..743456 as content while in the Data source I have selected ITAG2.4 Release: genomic annotations and press search.

What server returns me is:

The landmark named SL2.40:723456..743456 is not recognized. See the help pages for suggestions.

So, what am I doing wrong ? Is there any other method to look for that info, or we cannot do such a search?

Thank you

Answer 1

[Surya Saha]

Hello Frank,

There is a problem with your search string. You are using "SL2.40:50532..53532" which has 2 issues. ITAG2.4 is using the latest tomato genome build 2.50. The chromosome is also missing. An example of a correct search term is "SL2.50ch08:2626000..2648999". In case you are interested in ITAG2.40, the search string will be "SL2.40ch08:2626000..2648999". Please let me know if you have any more problems.

-Surya

[arronar]

Thank you very much. Do you know also if there is any API (for programming) to use for SOLgenomics ?

[Surya Saha]

We do not offer an API for SGN web services although we may consider that in the future is there is sufficient demand and capacity.