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Which Aligment Tool Do You Use To Find Rna Orthologs

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

rna orthologues human mouse
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updated by Leszek Leszek • written by Tonig Tonig

2 answers

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.

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written by Leszek Leszek

Thanks, I'll try it"

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written by Tonig Tonig

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.

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written by Asaf Asaf

Thanks, I'll take a look to Infernal also

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written by Tonig Tonig

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