How to detect antibiotic resistant gene from a genome ?
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What do you mean? You have so many ways for a bacterium (I guess you are working with bacetrial genomes) to be resistant to an antibiotic... Some ponctual mutations on ribosome (for example) give resistance...
You can start by making your own database of the known "antibiotic resistance" genes... and use blast against your genome of interest.
If your question if about discovering new gene, then, I am afraid Bioinformatics can not help you there... but good news, Biology can
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thanx for your reply....
Yes...I'm working on an unknown bacterial genome and I want to detect the antibiotic resistant genes present in it. So far I have used-Comprehensive Antibiotic Resistance Database (CARD) for this purpose..!!!
Can you suggest any more tools for detecting antibiotic resistant genes..Comment
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In addition to building your own databases and using BLAST/HMMs, it might be worth checking some available antibiotic resistance gene databases that are already out there such as: http://ardb.cbcb.umd.edu/.
KaraComment
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Other options would be ResFinder (https://cge.cbs.dtu.dk//services/ResFinder/) and Arg-Annot (http://aac.asm.org/content/58/1/212.full), though both use data from the ARDB and CARD databases, so they should not give you very different results, though they will be a bit more user-friendly.Comment
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