Blastn for gRNA characterization in ANopheles

Question

[Sbrillo]

Hi!

I'm trying to blast a dataset of gRNA against all the sequences present on the NCBI coming from Anopheles gambiae species. This is the script that I used:

blastn -db nt -query candidategRNA.fasta -task blastn-short -remote -evalue 10 -entrez_query 'Anopheles gambiae [organism]' -outfmt 6 -out G3-ill-G3-Nano-results.table 

Blast is creating the output file but it's empty... I already tried to blast my gRNAs manually and I always found matches with the web-browser Blastn version....

There is a way to use blast against all the sequences belonging to a specific organism and not just against the reference genome assembly (in my case Agamp3) ?

Or do you know how I can create my local database importing all the sequences belonging to Anopheles in the NCBI archive?

Any suggestions?

Thanks in advance!

Answer 1

[GenoMax]

Instead of entrez_query can you try limiting search using -taxids 7165 (which is the taxID of Anopheles gambiae). If that does not work you can try -taxids 7164 (which is Anopheles genus).

[Sbrillo]

Thanks a lot!

I have the output file with all the info that I needed, I will try to expand my blast result to Anopheles genus as you suggested :)

I have another question...

My input file contains more than 200 possible target sites and the output is quite big.

Do you have any suggestions on how to create a nice Plot of the results using R?

Thanks in advance

[GenoMax]

Don't what kind of plot you are looking for since some of it may depend on output format of your blast results. Came across this via a search see if it is useful: https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-020-00361-y