Can anyone tell me what to do after getting a large no. of ORF of newly bacterial sequence which has not yet been submitted to NCBI. Please tell me how to analyze large no. of contigs for their functional annotation?
How about using Prokka? It's a great tool, both from the scientific and from the software engineering POVs. Plus, if you don't like black boxes (aka RAST) should be the way to go.
quick answer RAST:
(If you plan to submit your contings to NCBI, RAST results will not be accepted. NCBI will automatically annotate your contigs from scratch, but you can start work with RAST annotations)
Use pipelines for annotate them and get categories such as COG, GO and so on.
You will get an overview of the physiological features of your organisms.
RAST is a good and quick solution.There are many posts on this topic:
Hi, If its "newly bacterial sequence" and not available in database. You should Predict the CDs after all you need to blast to publicly available database such ad swissport or NCBI to get a functional annotation of all the gene.
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Agree with @Israel Barrantes. I use it and I found IT really nice. Moreover, I like that for uncertain proteins I often got "hypothetical" as annotation, which I think is much less misleading than a wrong assignment as often happens with other tools.
Hi @dago i hope prokka is better choice than other due to its accuracy and time. But if its a newly sequence bacteria then could you get satisfactory result. I am little confused ??
For sure you get satisfactory results. Also, it is really fast. What I wanted to say is that sometimes with other annotation pipeline you get some kind of over annotation. Then, if the downstream analyses you do are based only on the annotation you can get misleading results.