This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Unable to view blastn result in blast2GO, Please help

I am working on MiRNA seq data analysis. I have completed the preprocessing steps and blastn search was performed against plant mature MicroRNAs from miRBase using the strategy "format and blast a fasta file and import blast results into Blast2GO".

So currently I have an xml file as the output of blastn operation. Now I just need to visualise the data within this xml file. I loaded this file to Blast2GO, but can't view any results. Isn't it possible to view the xml data in a better way by using Blast2GO

rna-seq
• 3,504 views • link
updated by Ram Ram • written by anjalinair20 • anjalinair20

1 answer

Could you please explain little more in detail what you are looking for and what you mean by "visualise the data".

In Blast2GO you can load XML or JSON Blast results and generate summary chart statistics like e-value distribution, similarity distribution or species distribution.

But if you are looking for functional annotation of your microRNA sequences based on the top blast hit against the miRBase you could use the "Export Top Blast Hit" or "Generic Export" function in Blast2GO and continue from there.

If you were looking for functional annotation with Blast2GO you would need to blast against a protein database (blastp) which can be linked/mapped by Blast2GO with the Gene Ontology. Not your case when working with a miRNA dataset, I guess ...

• 0 views • link
updated by Ram Ram • written by Stefan • Stefan

Log in to answer this question.

More posts like this