I am trying to find a convenient way to download, in batch, the FASTA sequence for as many bacterial orthologs of a gene that I can. I have tried using the E-utilities to access NCBI, and I can successfully search the database and retrieve gene IDs, but cannot progress further.
For what it is worth, here is the main part of PHP code I used to get this far (which can be seen in action at http://djcamenares.x10.mx/testing/parse1.php):
$startUrl="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=alaS&retmax=10000&usehistory=y";
$xml1=simplexml_load_file($startUrl) or die("Error: Cannot create object");
foreach ($xml1->IdList->children() as $child1)
{
$newUrl1="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=protein&id=" . $child1;
echo $newUrl1 . "
";
};
The code spits back a list of the links for the next step, but I can't seem to get them to work (for example, dumping them into $xml2=simplexml_load_file($newUrl1) or die("Error: Cannot create object"))
Any programming fixes, or knowledge of other databases, would be helpful. Interested primarily in prokaryotes.
http://djcamenares.x10.mx/testing/parse1.php
Hello Devin,
you can try using the ClustalW, which takes an alignment progesivo both DNA and protein
I send some links
http://align.genome.jp/
http://www.clustal.org/
http://www.ebi.ac.uk/Tools/msa/clustalw2/
http://web.archive.org/web/20101205192722/http://www.ebi.ac.uk/Tools/msa/clustalw2/
hits
Hi Devin,
If you have the links, paste them into a text file and use
wget -i [file.txt] -P [output directory]
this should download them to the specified directory
Hello Devin,
you can try using the ClustalW, which takes an alignment progesivo both DNA and protein
I send some links
http://align.genome.jp/
http://www.clustal.org/
http://www.ebi.ac.uk/Tools/msa/clustalw2/
http://web.archive.org/web/20101205192722/http://www.ebi.ac.uk/Tools/msa/clustalw2/
hits
There are lots of ways to do this, and while a programmatic script based approach might serve you better in the long run, there are actually some pretty quick ways to download these directly from a number of databases.
- The bacteri ensembl server (http://bacteria.ensembl.org/index.html) has an option to view orthologs once you have found a gene of interest. However, these lists can be incomplete.
- The results of a web-based NCBI BLAST search are downloadable. Although finding the right download option can be a little difficult to discover right away, it is right there on the results page. You can set your search to only look within the taxa of bacteria, set your max results as high as 10,000, fine-tune your E-value, etc.
- Biopython is very handy for this sort of query as well, and there are lots of example scripts out there.
Thanks for the answers everybody. I also found another option, that at least aids in the programmatic solution: NCBI's ebot (http://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi)
It generates a PERL script to the user's specifications for a pipeline of requests using NCBI's e-utilities. It's a nice solution for those with limited or no programming experience.
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