Question: Retrieving of all the sequences of a microbiome
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gravatar for Helder Gomes
3.7 years ago by
Helder Gomes10
Helder Gomes10 wrote:

Hi! I need to retrieve ALL the sequences of the microbiome of a specific organism (X. testudinaria). What do you think is the best way?

sequence ncbi • 1.0k views
ADD COMMENTlink modified 3.6 years ago by Daniel3.7k • written 3.7 years ago by Helder Gomes10

Most of the microbiome database I know are for H.sapiens. You can look for publications that pertain to your questions and see where the data exists online; or it may lead to a collaboration or a new experiment. Good luck! http://hmpdacc.org/reference_genomes/reference_genomes.php

ADD REPLYlink written 3.7 years ago by QVINTVS_FABIVS_MAXIMVS2.2k

Thanks QVINTVS_FABIVS_MAXIMVS. I don't need an actual database... 'just' the complete set of sequences of all of the microorganisms found in X. testudinaria. I've download the BLAST microbial 16S database through Perl. I'll start there.

ADD REPLYlink written 3.6 years ago by Helder Gomes10
1
gravatar for Daniel
3.6 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

You would be better finding papers which have produced the data you're looking for and seeing where it has been uploaded (or if it hasnt, ask them for it).

There is a repository for microbiome data at http://qiita.microbio.me/ which you can download from but I don't know if they have your organism, and it's not the most easy to navigate.

ADD COMMENTlink written 3.6 years ago by Daniel3.7k

Thanks Daniel. As I've just answered a.polo I am trying to run a Perl script that is almost working. If I don't manage to get the dataset I'll try QIITA.

ADD REPLYlink written 3.6 years ago by Helder Gomes10
0
gravatar for a.polo88
3.7 years ago by
a.polo88100
Italy
a.polo88100 wrote:

http://www.ncbi.nlm.nih.gov/gquery/?term=+testudinaria perhaps.

 

ADD COMMENTlink written 3.7 years ago by a.polo88100

Thanks a.polo88 but i've tried that way. The problem is that when I try a more focused search (http://www.ncbi.nlm.nih.gov/gquery/?term=xestospongia+testudinaria) I end up with a very limited number of sequences actually belonging to the microbiome.  

ADD REPLYlink written 3.6 years ago by Helder Gomes10
0
gravatar for a.polo88
3.6 years ago by
a.polo88100
Italy
a.polo88100 wrote:

ok if i have understood well the problem is that actually the studies are focused on the Human Microbiome project. and perhaps the lower number of sequences is due to no data for all of the organisms and reflect the few studies. perhaps a solution is test every of these sequence with a BLAST search.

 

ADD COMMENTlink written 3.6 years ago by a.polo88100
1

There are still to many sequences to run each one on BLAST. I am trying to run a script on Perl that is almost working. I am managing to retrieve the sequences... i am just not managing to get them on a document. Thanks!

ADD REPLYlink written 3.6 years ago by Helder Gomes10
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