RNAMotif

Tom Macke's suite of programs for RNA motif searches using motif descriptors rnamotif.

The latest code can be found here.

Descriptor Format

   emax = -12;
 
 descr
   h5( minlen=4, maxlen=7 )
     ss( len=4 )
   h3
 
 score
   { sc1 = efn( h5[1], h3[NSE] );
     if( sc1 > emax )
     REJECT;
     sc2 = length( h5[1] );
     SCORE = sprintf( '%.3f,%d,%s', sc1, sc2, ss[2] );
   }

Raw Output Format

#RM scored
#RM descr h5 ss h3
#RM dfile sprintf.strict.descr
>gi|173609|gb|M28984|ACARRDX A.castellani 5S ribosomal RNA
gi|173609|gb|M28984|ACARRDX -12.500,6,gcga 0      81   16 gggtgg gcga ccaccc
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -15.400,6,gaaa 0     110   16 ccccgg gaaa ccgggg
>gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
gi|1236163|gb|L41047|ANNRRO -12.100,5,gaaa 0     111   14 cccgg gaaa ccggg
>gi|173741|gb|M83548|AQF16SRRN Aquifex pyrophilus 16S ribosomal RNA (16S rRNA)
gi|173741|gb|M83548|AQF16SRRN -15.400,6,gaaa 0     154   16 ccccgg gaaa ccgggg
...

References

<biblio>

1. rnamotif pmid=11713323

</biblio>