How to download constitutive coding exon sequences for a list of 200 genes in the mouse genome?

Question

[spring_tan]

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.

[natasha.sernova]

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

Answer 1

[WouterDeCoster]

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?