Obtaining nucleotide gene sequence of bacteria using eutils

jpearl01 · 03-15-2014, 11:07 PM

Hi All,

I'm trying to write a quick program to download a bunch of genes' dna from bacteria. I don't have ids for the genes, just their protein names (like lacz or what-have-you). So use esearch to look for say the lacz bacteria gene from the gene database:

http://eutils.ncbi.nlm.nih.gov/entre...p+AND+bacteria[filter]

then, I grab the first id in the list that is returned, and convert it from a gene id to a nucleotide using elink

http://eutils.ncbi.nlm.nih.gov/entre...tide&id=945006

Which gives back a list of different ids. Most of the ids (using efetch to get the sequence) generally give back the entire genomic sequence of the organism it was found in. *sometimes* one of the id's gives back the actual gene nucleotide data, but not always. For example the first two ids from the above elink result give whole genomic sequence:

http://eutils.ncbi.nlm.nih.gov/entre...&rettype=fasta

The third id gives the gene sequence:

http://eutils.ncbi.nlm.nih.gov/entre...&rettype=fasta

So, what gives? Is there a way to tell which ones are whole genome sequences, and which are gene sequences? Maybe an elink parameter?

~josh

TiborNagy · 03-17-2014, 06:51 AM

Try to download the sequences in GeneBank format and parse the descriptions.

jpearl01 · 03-17-2014, 11:05 AM

Well, that is a possibility. However, I would really like it if I didn't have any intermediary steps. What is frustrating is that if I do the same search, but then link to the *protein* database, I get the correct AA sequence almost every time. I'm not sure why I can do that for the protein sequence but not for the nucleotide. Really, I'm wondering if I'm doing something wrong.

gringer · 03-17-2014, 01:04 PM

Note that NCBI has now released Entrez Direct, which has pipeable functionality for downloading via Entrez. There is likely a specific query that can be fed into Entrez direct for the bacterial genomes.

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03-15-2014, 11:07 PM	#1
jpearl01 Member Location: Philadelphia PA Join Date: Dec 2010 Posts: 17	Obtaining nucleotide gene sequence of bacteria using eutils Hi All, I'm trying to write a quick program to download a bunch of genes' dna from bacteria. I don't have ids for the genes, just their protein names (like lacz or what-have-you). So use esearch to look for say the lacz bacteria gene from the gene database: http://eutils.ncbi.nlm.nih.gov/entre...p+AND+bacteria[filter] then, I grab the first id in the list that is returned, and convert it from a gene id to a nucleotide using elink http://eutils.ncbi.nlm.nih.gov/entre...tide&id=945006 Which gives back a list of different ids. Most of the ids (using efetch to get the sequence) generally give back the entire genomic sequence of the organism it was found in. sometimes one of the id's gives back the actual gene nucleotide data, but not always. For example the first two ids from the above elink result give whole genomic sequence: http://eutils.ncbi.nlm.nih.gov/entre...&rettype=fasta The third id gives the gene sequence: http://eutils.ncbi.nlm.nih.gov/entre...&rettype=fasta So, what gives? Is there a way to tell which ones are whole genome sequences, and which are gene sequences? Maybe an elink parameter? ~josh

03-17-2014, 06:51 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	Try to download the sequences in GeneBank format and parse the descriptions.

03-17-2014, 11:05 AM	#3
jpearl01 Member Location: Philadelphia PA Join Date: Dec 2010 Posts: 17	Well, that is a possibility. However, I would really like it if I didn't have any intermediary steps. What is frustrating is that if I do the same search, but then link to the protein database, I get the correct AA sequence almost every time. I'm not sure why I can do that for the protein sequence but not for the nucleotide. Really, I'm wondering if I'm doing something wrong.

03-17-2014, 01:04 PM	#4
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	Note that NCBI has now released Entrez Direct, which has pipeable functionality for downloading via Entrez. There is likely a specific query that can be fed into Entrez direct for the bacterial genomes.