Question: Blastp to know the name of the protein
0
gravatar for utkarsh.sood
3.4 years ago by
utkarsh.sood30
India
utkarsh.sood30 wrote:

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 blast genome • 860 views
ADD COMMENTlink modified 3.4 years ago by Michael Dondrup46k • written 3.4 years ago by utkarsh.sood30
0
gravatar for Michael Dondrup
3.4 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

1. 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.

 

 2. 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.

ADD COMMENTlink written 3.4 years ago by Michael Dondrup46k

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.

ADD REPLYlink written 3.4 years ago by utkarsh.sood30
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