Question: How to compare contigs with an existing protein from a species ?
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gravatar for carerjose
4.1 years ago by
carerjose0
Canada
carerjose0 wrote:

I have a few contigs and I need to compare them with a known protein of a species. I dropped the contigs in BlastX and since I got very low e-values, I need arrange and assembly them in order that the consensus of the contigs seems very similar to the know protein sequence. 

Is there any software or written tutorial that can simplified this process? 

I was thinking about using a software that can allow to align all the contigs that I have and download the DNA sequence of the reference protein. 

dna blastx sequence contig • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.1 years ago by carerjose0

Is nto really clear what you wnat to do. You have contings, do you want to predict ORF in them and look if among the ORFs there are specific protein of interest?

ADD REPLYlink written 4.1 years ago by dago2.5k

Yes, that would be of so much help. 

ADD REPLYlink written 4.1 years ago by carerjose0

Can you provide more details, which organism are you working with?

ADD REPLYlink written 4.1 years ago by dago2.5k
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