Question: How to download constitutive coding exon sequences for a list of 200 genes in the mouse genome?
0
gravatar for spring_tan
4.1 years ago by
spring_tan0
Edinburgh, Scotland
spring_tan0 wrote:

Hi all,

I am a complete newbie in the world of bioinformatics. A molecular biologist by training and working 95% of the time at the bench, I am trying to learn how to download exon sequences that are expressed in all tissues for a list of 200 mouse genes and save them into a single FASTA file. I want to then scan for certain motifs in these sequences in a batch mode by feading the FASTA file into an online program.

So far, I have been trying to use the Entrez.efetch function in Biopython to fetch the infomation for a single gene and then use a loop function to download all the sequences from ncbi. Could some one tell me if I am heading in the right direction and could you help me out as I am stuck and not getting it to work... If not, could you point me to the right direction?

Many thanks in advance.

sequence gene genome • 842 views
ADD COMMENTlink modified 4.1 years ago by WouterDeCoster44k • written 4.1 years ago by spring_tan0

Look at these posts.

A: Online Resources For Mouse Research

The post is 4 years old, but many links are still alive.

There are two directories in NCBI for two different mouse strains:

ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/latest_assembly_versions/

Recent mouse RNA-prot data from NCBI can be found here :

ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot/

You will have to learn about this browser :

https://genome.ucsc.edu/goldenpath/help/hgTracksHelp.html

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by natasha.sernova3.7k
0
gravatar for WouterDeCoster
4.1 years ago by
Belgium
WouterDeCoster44k wrote:

So you already have your list of mouse genes? Using Biopython and Entrez.efetch sounds like an okay way to go. Have you seen the Biopython tutorial and cookbook? http://biopython.org/DIST/docs/tutorial/Tutorial.html

What exactly doesn't work?

ADD COMMENTlink written 4.1 years ago by WouterDeCoster44k
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: 696 users visited in the last hour