How to search for a protein sequence of an specific taxa in NCBI?

Question

[ehsansepahi]

My example: Sequence of HBB (Hemoglobin Beta) in Fishes.

How can I do a good search to obtain above sequences?

Answer 1

[GenoMax]

NCBI Home --> Search for "Haemoglobin beta" --> Select Proteins/DNA --> Results by taxon (right hand pane) --> Find the Fishes in the list/tree

[ehsansepahi]

Thank you. But assume that I don't know all fishes scientific name, and its a long list. what is the smarter way?

[GenoMax]

If you are not interested in particular fish and there are many you can add these filters to the left page under species (click on customize button)

--> type "fish" in search window and then select teleost, ray-finned, catilaginous, bony, puffer and lobe-finned fish, as fish types.

A search term would look like this: (haemoglobin beta[Protein Name] OR (haemoglobin[All Fields] AND beta[All Fields])) AND "cartilaginous fishes"[ORGN]

PS: You can also look at efetch utilities (http://www.ncbi.nlm.nih.gov/books/NBK25499/).

Answer 2

[Sej Modha]

NCBI eutils solution based on genomax2's suggestion

esearch -db protein -query "fish[orgn] AND haemoglobin beta[Protein Name] OR (haemoglobin[All Fields] AND beta[All Fields]) AND animals[filter]"|efetch -format fasta