Hi, i am trying to discover a desired motif in a set of 251 sequences but my results are not consistent. In some runs i get desired motif but in other runs it disappears. Now i am trying to find the motif with some motif as a seed in my DNAstringset object of sequences.

My seeded motif is given here is present in motif.txt file     

A    0.4619    0.927    0.8053    0.9305    0.4262    0.6623    0.4405    0.8018    0.7588    0.8912    0.7517    0.8268    0.4834    0.6158
C    0.0148    0.0077    0.0291    0.0148    0.3046    0.0112    0.022    0.0327    0.0148    0.022    0.0148    0.0184    0.0828    0.0291
G    0.1114    0.0148    0.0077    0.0291    0.0935    0.1221    0.0184    0.1078    0.0685    0.0148    0.1543    0.0291    0.1114    0.14
T    0.4119    0.0506    0.1579    0.0255    0.1758    0.2044    0.5192    0.0577    0.1579    0.072    0.0792    0.1257    0.3224    0.2151

Please tell me possible command to get similar motif to seeded motif in DNAstringset.

Hi Vinod,

rGADEM uses a genetic algorithm which can explain why you are getting different results with each run. Even if you give the algorithm a seeded motif, it will generate multiple new motifs by mutation and crossing-over each iteration. It's possible that the motif you are expecting does not produce the best score with the fasta sequences you are using and that in some run the rGADEM is able to find a better motif.

With genetic algorithms, it's a good idea to launch multiple runs to make sure the algorithm was not stuck in fitness peak.

Of course, it's not possible to know for sure without the original files and with the parameters used.