Download protein fasta files

It only takes a minute to sign up. Connect and share knowledge within a single location that is structured and easy to search. I'll be grateful if someone can help me. Thank you. As you have several sequences to download, I think it will be quite easy to add this command into a little bash script to process all of them.

For this, you can use Entrez Direct as mentioned by dc Why not always use Entrez Direct? While it is fine for a small number of sequences, it can be slow to download a large number of sequences.

Entrez Direct by default will download uncompressed data so you will end up spending more time downloading a larger file instead of downloading a smaller, compressed file from FTP more quickly. If you were to use Entrez Direct for this purpose, I'd not bother with a bash script and use epost to first post the entire list of accessions and then pipe it to efetch as shown below:.

You can also get this link directly, by using Chrome's developer tools F12 , viewing the Network tab, then loading the page in 1. Sorry, I can't post a comment with my reputation score. Genbank can do a similar thing for a set of DNA seqs. As explained here the code below first checks to see if you have these packages. If not, the missing packages are installed from CRAN and then loaded. OK, DNA sequences first. There are GenBank accession IDs in the file, each of which corresponds to a COI sequence from a species of wrasse or parrotfish or outgroup taxon.

These accession IDs were determined beforehand as being appropriate for the study. I have added line breaks to the sequence below to display this better:. Its easy enough to adapt the code if you wanted to output the protein names for example, or GI numbers. In such cases, you can first extract the nucleotide sequence see below and then translate it to get the amino acids. I've saved this one till last, because it was the hardest. Manually annotated polyA features overlapping the transcript 3'-end.

Pubmed ids of publications associated to the transcript from HGNC website. Amino acid position of a selenocysteine residue in the transcript. Source of the transcript annotation.