
Scores can be calculated using the M. jannaschii genome as background and the set of tRNA and rRNA ncRNA genes as target. 
Strands are treated symmetrically

	java SIGRS.SIGRSMain -BG seqs/Methanococcus_jannaschii_DSM2661.fa -TG seqs/Methanococcus_jannaschii_DSM2661_ncRNAs.fa -OUT Methanococcus_jannaschii_scores.sc -SYM T

Calculating scores but weighting the tRNAs and rRNAs equally

	java SIGRS.SIGRSMain -BG seqs/Methanococcus_jannaschii_DSM2661.fa -TG seqs/Methanococcus_jannaschii_DSM2661_ncRNAs.fa -OUT Methanococcus_jannaschii_scores_weighted.sc -SYM T -C tRNA rRNA

Searching one strand of the M. jannaschii genome assuming independent nucleotides. 
Expect threshold is set to 1.

	java SIGRS.SIGRSMain -IN seqs/Methanococcus_jannaschii_DSM2661.fa -S Methanococcus_jannaschii_scores_weighted.sc -OUT Methanococcus_jannaschii_search_M0.gff -M 0 -E 1 -L M0 -SYM T

Searching both strands of the M. jannaschii genome assuming Markov-dependent nucleotides. 
Expect threshold is set to 1.

	java SIGRS.SIGRSMain -IN seqs/Methanococcus_jannaschii_DSM2661.fa -S Methanococcus_jannaschii_scores_weighted.sc -OUT Methanococcus_jannaschii_search_M1.gff -M 1 -E 1 -L M1 -SYM F

Results of the commands above can be found in the following files:
./Methanococcus_jannaschii_scores.sc
./Methanococcus_jannaschii_scores_weighted.sc
./Methanococcus_jannaschii_search_M0.gff
./Methanococcus_jannaschii_search_M1.gff

