This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get pfam seed sequence taxonomy info?

Is there an easy(ish) way to get the taxonomy information for pfam seed sequences? For the life of me I cannot figure out any other way to do it than blasting each seed sequence and getting the top hit off of ncbi, which is ridiculous because pfam links to ncbi and vice-versa. Since pfam has the option for downloading sequences by taxa, surely this information is available.

For example: blasting a seed sequence for pfam000078 gets me to a genbank entry which leads me to this page: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=249567. And oh look, it links to pfam000078.... However, the actual ids for the seed sequences (e.g. RTJK_DROME/502-757) seem perfectly useless.

pfam blast taxonomy ncbi
• 3,278 views • link
updated by Ram Ram • written by beegrackle beegrackle

1 answer

Here is how I got taxonomy strings starting with a fasta seed alignment

  1. Get the list of accession IDs
    grep ">" seed.fasta | sed 's/>//' |cut -f1 -d'/' > pfamaccessioncodes.txt

  2. Upload your list (or copy and paste) into the Retrieve/ID mapping tool https://www.uniprot.org/uploadlists/

  3. Download a tab-separated version of your information. The data you want should be in columns 1 and 7.

• 0 views • link
updated by Ram Ram • written by jubillante • jubillante

Log in to answer this question.

More posts like this