RNAMotif

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Tom Macke's suite of programs for RNA motif searches using motif descriptors [1].

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

  1. Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, and Sampath R. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res. 2001 Nov 15;29(22):4724-35. PubMed ID:11713323 | HubMed [rnamotif]
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