downloading protein sequences

Question

[praveenhcu131]

i have a list of genes and i want to download the protein sequences of the all genes of mouse at a time using ncbi tool kit please help me in this issue?

[zx8754]

What have you tried? Maybe see this post: https://cran.r-project.org/web/packages/biomartr/vignettes/Sequence_Retrieval.html

Answer 1

[Bill Pearson]

Take a look at the slides in this link:

http://fasta.bioch.virginia.edu/biol4230/lects/biol4230_9_web_resources.pdf

Slides 4 - 7 show a general strategy for using NCBI's esearch/efetch sites to (1) look up the refseq protein accession for your genes using a search term (your gene name) and (2) download the protein sequences using the accession. Slide 7 does the entire process for a search term; you would like to substitute the line:

s_args = "db=protein&term=GSTM*+AND+human[organism]"+ \
               "+AND+srcdb_refseq[prop]&idtype=acc&retmax=1000";

for something where:

 "term="db=protein&term="+your_mouse_gene_name+"AND mouse[organism]" + ...

Other slides in the lecture describe other strategies from other resources, but if you want to use NCBI, you will need to do the two step esearch/efetch process.