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