Hello!
I'm very uncomfortable, but could you help me again. Let's see at this link http://www.ncbi.nlm.nih.gov/protein In menu Search (bee) AND "Apis mellifera"[porgn:__txid7460]. And choose 'RefSeq ( 10618 )' right of the screen (in the Filter menu).
We have 10 618 records. Let's click one of them. In here http://www.ncbi.nlm.nih.gov/protein/NP_001011614.1 we can see amino acid code of the protein. But click CDS link.
Ok. Now we can see nucleotide code of the protein. http://www.ncbi.nlm.nih.gov/nuccore/58585171?from=135&to=638&report=gbwithparts
Could you tell me, is it true that this code always starts with a triplet 'atg' and end termination?
Another question. There are 10618 records in this site. I need all of them in one ore some files. Do you know, BioPerl ( bioPython ) or Entrez Utilities can help to get it? Wich script? May be another programm? I need nucleotide code for all proteins foe each organism.
Thank.
Sorry for bad english.
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Gleb •
1 answer
You can download a list of ids with BioPerl and format them in fasta or GenBank or any of the other supported formats. There are example scripts for almost exactly what you describe in your question here.
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Gleb, I would suggest you read the Transcription and Translation (for genetics) articles on Wikipedia and the NCBI Eutils manual (all easily accessible via google).
I understand. Thank you. I just thought it was a simple little problem: how to download CDS... Probably not.
It is reasonably simple once you worked with the databases a couple of times. However, telling you how every step of how to do it (or writing a script for you that does it) might cause more harm than good when you need a slightly different dataset the next time. You are of course welcome to ask questions here when you are stuck.