I have an assignment from my PI professor to find a gene on a genome, he mentioned that I have to make sure that I have to annotate them first. Thing that confused me, there's a feature in Genome database of NCBI to BLAST it. Is the genome in the database already annotated?
I was then tBLASTn the genome and got the results that I want, but the statement by my PI to annotate it make me worried if I did it right. The genome is located on Genome database (note Nucleotide or SRA) and it mentioned that it has been assembled. I tried to annotate some of the contigs with the best BLAST results with Augustus. I re-BLAST them again, but the result number is reduced, and some have errors. Did I do it right?
Also, is the SRA-based genome already assembled? They often look messy. I tried to BLAST them, but NCBI BLAST interface stated that I can't BLAST it.
I suggest you talk with your PI. They clearly have something specific in mind.
I'm assuming you are looking to see if there is a gene(s) in the genome of your particular organism that could code for a given protein?
Good luck!
@Katie: Yes, he wants me to find a gene in some results of whole genome sequencing that code a transcription factor protein
Hi Adhityo. If you have the DNA sequence of the gene, you can "search" for it using a direct Blast against the assembly. In case you are interested in the coding sequence of the gene, you should do the annotation first. Hope it helped.
Good luck!
@Ricardo: Hi Ricardo, thanks for the answer. So basically to find the gene existance or to find a similar structures, we can just simply BLAST the assembly using cDNA (in BLASTn) or protein (in tBLASTn). But to find the whole CDS, annotation is required, right? Please correct me again of I wrong. My PI showed me his previous paper and it only shows that his previous student just use the sequence of a database to the genome assembly in NCBI.
If let’s say, I have the matching sequences from many reference sequence that I BLAST with (I used the genome assembly in NCBI Genome) and it pinpoint ordered sequences in only one scaffold/contig, how do people normally annotate the scaffold?
Adhityo, I have to understand a little bit better what you want to do, to answer. Can you please write me to [email protected]?
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