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Blastn for gRNA characterization in ANopheles

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!

anopheles ncbi grna blastn
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updated by GenoMax GenoMax • written by Sbrillo • Sbrillo

1 answer

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).

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written by GenoMax GenoMax

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

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written by Sbrillo • Sbrillo

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