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.
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written
by
spring_tan •
1 answer
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?
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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