Find defence related and disease resistant genes in Rice genome

Question

[vedikaa96]

Hi, I am a Ph.D student and have sequence of all chromosomes of Rice in FASTA format and I want to find more defence related and disease resistant genes (like Xa), proteins(R proteins, PRR) and QTLs (qBBR11-1). So, for this is performing functional annotation is the correct way to find? Also, for this purpose is using BLAST2 GO or WEGO Tool or GenSAS or Galaxy (Augustus)? If there are any other tools kindly suggest me.

Edit: Removed personal information.

[vedikaa96]

So, these GO numbers can be retrieved from the annotation data of all the rice species from NCBI ? Also, I have to find and study more such genes, proteins and QTLs which are not mentioned before, so, in this case I have to perform the annotation ?

Answer 1

[ashish]

Rice is already very well annotated, you don't need to do BLAST2GO, AUGUSTUS etc. You can look up the GO numbers for defence realated genes/pathways and just pull down all genes associated with those GO numbers using biomart at ensembl plants. You can also do some manual filtering after that to get a more refined list of genes.

[vedikaa96]

So, these GO numbers can be retrieved from the annotation data of all the rice species from NCBI ? Also, I have to find and study more such genes, proteins and QTLs which are not mentioned before, so, in this case I have to perform the annotation ?