Question: Retrieving Complete Cds From Ncbi
0
gravatar for Elmo
6.9 years ago by
Elmo110
Elmo110 wrote:

Hi,

I was trying to retrieve complete cds sequences from NCBI for a certain protein of interest, say acetyl coa transferase. I did an advanced search as below:

((("acetyl coa acetyl transferase"[Protein Name]) OR "acetyl coa acetyltransferase/3 ketoacyl coa thiolase"[Protein Name]) OR "acetyl coa/acetoacetyl coa transferase"[Protein Name]) AND "cds"[Feature key] complete

However, I got all the cds sequences, including the partial one as well, instead of only complete cds. Do I have to include something else in my advance search? Also, I did a BLAST search for that protein using a specific species, and I wish to retrieve complete cds sequences of other species having that protein as well. Is there a shortcut to obtain all the complete cds only or do I have to manually look into 1 by 1 of the BLAST results to check if those species having complete cds or not?

Please advice. =(

Thanking you in advance!

ncbi cds blast • 3.5k views
ADD COMMENTlink written 6.9 years ago by Elmo110
1

Where did you do this search? I tried entering it exactly as you gave it, in http://www.ncbi.nlm.nih.gov/protein, and I got three results (here: http://tinyurl.com/7vwp3a6) and all seem to be complete sequences.

ADD REPLYlink written 6.9 years ago by Chris Maloney330
0
gravatar for SES
6.9 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

Try searching the UniGene database. For example, search for Acetyl-coenzyme A, then click the links next to the species of interest and download whatever you need, protein sequence, nucleotide sequence, conserved domains, etc. See the query tips page for advice on formatting your search.

ADD COMMENTlink written 6.9 years ago by SES8.1k
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