Question: How to find the gene that a site of mouse genome belongs to?
0
gravatar for yinzl2007
3.8 years ago by
yinzl200720
China
yinzl200720 wrote:

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?

site of gene mouse genome • 1.1k views
ADD COMMENTlink modified 3.8 years ago by Sean Davis25k • written 3.8 years ago by yinzl200720

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

ADD REPLYlink written 3.8 years ago by Sean Davis25k

The format is .fa 

ADD REPLYlink written 3.8 years ago by yinzl200720
2
gravatar for cyril-cros
3.8 years ago by
cyril-cros890
France
cyril-cros890 wrote:

Use the UCSC Genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=456934153_5jN1pHsO20ln0XuE8wrxgyjlA25w&clade=mammal&org=Mouse&db=0 ). 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.

ADD COMMENTlink written 3.8 years ago by cyril-cros890

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.

ADD REPLYlink written 3.8 years ago by yinzl200720

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.

ADD REPLYlink written 3.8 years ago by cyril-cros890
2
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Sean Davis25k

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.

ADD REPLYlink written 3.8 years ago by yinzl200720

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

ADD REPLYlink written 3.8 years ago by Sean Davis25k
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