How to find the gene that a site of mouse genome belongs to?

Question

[yinzl2007]

I have the genome data of mouse which downloaded from UCSC, but I don't know which gene the site belong? So how can I find out which gene a site belongs to?

[Sean Davis]

What is the "genome data" that you have? In what format is it?

[yinzl2007]

The format is .fa

Answer 1

[cyril-cros]

Use the UCSC Genome browser. If you have a not too big genomic interval (chromosome start_position end_position), you can take a look at what it contains.

If this interval is too wide, I am sure someone will provide you with a script to get all the genes near various regions.

[yinzl2007]

Thanks for your answer!

The tools on line can help me check the gene on line. What's more, I want to deal with my data in my local server. Is there any map tools (or software package) I can use in my local server? So I can deal with my data in my own computer. It's better in Python laguage. Thank you again.

[cyril-cros]

You have what is called the UCSC table browser, and annotation files which are either in the .bed or .gtf format. You can also get them from Ensembl. You can view them in the IGV software (Integrative Genome Browser). These annotations define intervals in your .faa genome sequences, corresponding to features like exons, introns, CDS or isoforms. You can manipulate them with software like Bedtools or Bedops, which have Python bindings (pybedops module for example). It depends on what you want to do.

Answer 2

[Sean Davis]

Since your genome data is fasta (.fa), you'll need to use a tool like BLAST or blat to align the sequence to something known. The blat tool is here:

https://genome.ucsc.edu/cgi-bin/hgBlat

Just paste in your sequence, choose the right genome, and hit submit. You can then review the results in the UCSC genome browser.

[yinzl2007]

Thanks for your answer!

The tools on line can help me check the gene on line. What's more, I want to deal with my data in my local server. Is there any map tools (or software package) I can use in my local server? So I can deal with my data in my own computer. It's better in Python laguage. Thank you again.

[Sean Davis]

There are many, including blat. Mapping tools are written in compiled languages (not python), generally.