Annovar data base

Question

[lamlam]

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

Answer 1

[natasha.sernova]

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...

Answer 2

[lamlam]

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

[Benn]

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.

[lamlam]

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

[Benn]

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.