How can I interpret rpoB gene sequencing results?
I have sequenced rpoB gene of 10 MDR Mycobacterium tuberculosis isolates, could anyone help me to interpret these results using bioinformatics database?
There are a lot of rpoB sequences (full length and fragments) in the NCBI nr database, and a lot of full length sequences in the RefSeq database.
What do you mean 'interpret'? If all you need to do is a classification then it would be as simple as using the NCBI online BLAST service. If you want to do some phylogenetic analysis, as far as I know there are no dedicated rpoB databases so you'll need to create your own from one of those repositories and then work through a standard alignment/tree-building pipeline.
Interpretation is a very vague term, you can do quite alot with a gene sequence, it all depends on your objectives. For instance if you are interested in identifying what exactly you sequenced, you could perform a BLAST analysis to identify closest neighbours. Going deeper, you could maybe want to see how your MDR strains relate with pre-existing stains already deposited in your organism-specific database, or straight out of (ncbi)genbank, and run a phylogenetic analysis. As I said, there's so much you would want to do with a sequence, it totally depends on your research questions.
using blast , multi sequence alignment software,find mutation using these software
Did you sequenced the entiry rpoB sequence of only the 81 bp hotspot region, in which 95% of all mutations are leading to rifampicin resistance. If you only sequenced the hotspot region you can easily do a bit of SNP search with your 10 strain with the basic analysis software. All the different rpoB mutations are well described.
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