Which Aligment Tool Do You Use To Find Rna Orthologs

Question

[Tonig]

I am interested to find orthologous long non coding RNAS lncrnas between Mouse and Human and I am wondering which is the best method to use, Imean, is there one RNA aligner that detects long non coding regions?

Thanks

Answer 1

[Leszek]

You can give a try to BlastR - A tool for searching and clustering RNA.
It has improved sensitivity compares to blast (use of contact information) and it's as fast as blast.

[Tonig]

Thanks, I'll try it"

Answer 2

[Asaf]

I'm not familiar with such a tool but I can think of two strategies:[?] 1. Use Infernal although it should base on sequence and structure I think it can be useful.[?] 2. Run any local alignment algorithm and change the substitution matrix so structure conserving changes (i.e. T<->C and A<->G) will get a score somewhere between a match and a mismatch.

[Tonig]

Thanks, I'll take a look to Infernal also