miranda - Input short sequences, but... (Jun/17/2005 )

Hi,

Input fasta file number 1 is supposed to be the short mature miRNA, right?

When I use this input i however do not get any output from miranda (run through java)

When input fasta file number one is pre-miRNAs i can see that the program is running.

Anyone think of an explanation?

/Calle

-Calle-

Are you setting the criteria too high? You got hits with pre-miRNA probably because the program may use other area of the sequence (not the muture miRNA) to find matches (I am not sure if this is the case, but I know for sure muture miRNA sequence in FASTA is expected by the program).

-pcrman-

Thanks for the input pcrman,

I was thinking about the parameters.. and have tried a lot of different ones.. still the same output.

Could anyone please suggest parameters that should generate output i.e non stringent parameters?

Thank you in advance

/Calle

-Calle-

The default parameters are low enough. I usually have to raise the score threshold from 80 to 120. Try a bunch of UTR sequences to get a feeling how it works.

-pcrman-

Thanks for further input,

The problem was in the fasta file I used ffor my mirna sequences.. I copied them and pasted them into the example bantam-fasta file and I was clear.. Don´t ask me what was wrong.. Furthermore I switched to the cygwin version..

I will take a look at the parameters further, the scale parameter seems helpful..

/Calle

QUOTE (pcrman @ Jun 20 2005, 07:45 PM)

The default parameters are low enough. I usually have to raise the score threshold from 80 to 120. Try a bounch of UTR sequences to get a feeling how it works.

-Calle-