ANN: NCBI EUtils client
We have developed a client-side interface to NCBI's "EUtils" server, which is a web service for querying their Entrez databases, including GenBank and PubMed.
It is available from http://www.dalkescientific.com/EUtils/ and distributed under the Biopython license, http://www.biopython.org/License.shtml
Example: Get all protein sequences related to protein GI:4579714
import EUtils from EUtils import HistoryClient client = HistoryClient.HistoryClient() result = client.post(EUtils.DBIds("protein", "4579714")) related = result.neighbor_links("protein") related_dbids = related.linksetdbs["protein_protein"].dbids proteins = client.post(related_dbids) len(proteins)
223
infile = proteins.efetch(retmode = "text", rettype = "fasta")
fasta = infile.read() print fasta[:788]
gi|27450749|gb|AAO14677.1|AF508258_1 rhodopsin [Pyrocystis lunula]
MAPIPDGFTYGQWSLVYNSLSFGIAGMGCATIFFWLQLPNVSKSYRTALTITGLVTAIATYHYVRIFNSW VDAFKVVNVNGGDYTVTLLGAPFNDAYRYVDWLLTVPLLLIELILVMKLPKAETVKLSWNLGVASAVMVA LGYPGEIQDDLLVRWFWWAMAMIPFYYVVVTLVNGLSDATAKQPDSVKSLVVTARYLTVISWLTYPGVYI IKSMGLAGNIATTYEQVGYSVADVVAKAVFGVLIWAIAAGKSDEEEKNGLLG
gi|6319528|ref|NP_009610.1| Homolog to HSP30 heat shock protein Yro1p;
Yro2p [Saccharomyces cerevisiae] MSDYVELLKRGGNEAIKINPPTGADFHITSRGSDWLFTVFCVNLLFGVILVPLMFRKPVKDRFVYYTAIA PNLFMSIAYFTMASNLGWIPVRAKYNHVQTSTQKEHPGYRQIFYARYVGWFLAFPWPIIQMSLLGGTPLW QIAFNVGMTEIFTVCWLIAACVHSTYKWGYYTIGIGAAIVVCISLMTTTFNLVKARGKDVSNVFITFMSV IMFLWLIAYPTCFGITDGGNVLQPDSATIFYGIIDLLILSILPVLFMPLANYLGIERLGLIFDEEPAEHV GPVAEKKMPSPASFKSSDSDSSIKEKLKLKKKHKKDKKKAKKAKKAKKAKKAQEEEEDVATDSE
Andrew Dalke dalke@dalkescientific.com
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Andrew Dalke