How can I create a miRNA:mRNA alignment figure?

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Vishal Sarsani

You can try using gff2ps

http://genome.crg.es/software/gfftools/GFF2PS.html

We generated following figure using gff2ps

Goldi A Kozloski

Thank you Vishal, I appreciate your help, but I was looking to the sequence alignment (bases). I can get the miRNA:mRNA (WT) from most target prediction algorithms, but not for a Mutated mRNA sequence. I can do it by hand, but just wanted to know if there was a tool that I can use to facilitate this.