Question: Annovar data base
0
gravatar for lamlam
3.0 years ago by
lamlam10
lamlam10 wrote:

Hello We use annovar for annotation mycobacterium tuberculosis i want Data base for Myco tuberculosis ? plz give a link for download database

next-gen annotation • 911 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by lamlam10
1
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

What exactly do you need?

There are at least several of such DBs.

http://mycobacterium.biocyc.org/

http://www.sanger.ac.uk/resources/downloads/bacteria/mycobacterium.html

http://www.tbdb.org/

This is a paper about TB, 2009:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686437/

This is another paper, it is from 2012:

http://database.oxfordjournals.org/content/2014/bau035.full

It is something like a list of all existing now-a-days TB-databases:

https://bioinformatictools.wordpress.com/tag/mycobacterium-tuberculosis/

It's a recent paper about TB-variation DB:

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-308

A paper about TB-divergence DB:

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-373

A paper about TB drug-resistance DB:

"MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis".

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-107

Unfortunately there are even more than these DBs...

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
0
gravatar for lamlam
3.0 years ago by
lamlam10
lamlam10 wrote:

i need the right Data Base for using annovar for mycobacterium tuberculosis ! And i want to know how to download it when i used http://www.sanger.ac.uk/resources/downloads/bacteria/mycobacterium.html with command line: $ perl annotate_variation.pl --downdb --webfrom http://www.sanger.ac.uk/resources/downloads/bacteria/mycobacterium.html /path/annovar/humandb i have an error on run

ADD COMMENTlink written 3.0 years ago by lamlam10

Are you sure ANNOVAR is the right tool for your bacterium? I mean I have used ANNOVAR to annotate variants (mutations) in human, and to get SNP information, and allele frequencies, etc.

I cannot exactly see how this would be interesting for Mycobacterium samples? What is it exactly what you want to do, please tell more about your experiment and goals.

ADD REPLYlink written 3.0 years ago by Benn6.6k

i try to use an other tools like Gatk and snpEff for detect the location of snp's and indels in the genes of mycobacterium tuberculosis; for these tools i need a data base for MTB? do you suggest me an other tool special for mycobaterium tuberculosis

ADD REPLYlink written 3.0 years ago by lamlam10

No I didn't suggest anything, sorry, I am just trying to think along with you.

I don't work with bacterial data, only human or mouse mostly. But I can't imagine that a bacterial species like Mycobacterium tuberculosis would have a SNP database for all variants in the 'population', which is comparable to dbSNP for humans. In this dbSNP allele frequencies of populations are reported, for thousand of individuals. I don't know how many individual strains of mycobacterium are sequenced, and if they are all well reported in a database which can be used by your desired programs.

ADD REPLYlink written 3.0 years ago by Benn6.6k
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