Blastp to know the name of the protein
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5.9 years ago
utkarsh.sood ▴ 40

Hello

I wanted to know the name of the proteins encoded by a plasmid. For this, I am using blastp to blast the .faa file generated using Fraggenescan against the local nr database using commandline. I have two queries:

1. Is this the right way to solve my problem?

2. which output format I should select to have proper visualisation of the results?

 

Thanks!

myposts genome blast • 1.3k views
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5.9 years ago

Is this the right way to solve my problem?

Possibly not, but depends on many factors, you are not giving us enough info. Where does the sequence come from, is it already annotated? Why do you need to use fraggenescan if you have a halfway ok assembly of a (bacterial?) plasmid, is it really fragmented? Likely it is not the only right way (that doesn't exist), nor the best way.

which output format I should select to have proper visualisation of the results?

If you don't know what you will need in the future use default or asn1. Don't use tabular.

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The sequence is generated by SMRT sequencing of a bacterial plasmid. The sequence was annotated using RAST server, but it shows that 50% of the proteins are hypothetical proteins.

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