Difference: SupplementRiboswitchPrediction (2 vs. 3)

Revision 32009-06-21 - JeffreyBarrick

Line: 1 to 1
META TOPICPARENT name="SupplementList"

Predicting Riboswitch Regulation on a Genomic Scale

Line: 69 to 69
 >fragment_db.pl -s 40 /db/refseq24/fasta /db/refseq24/fragment
 >cmbuild TPP.cm TPP.sto
 >cmcalibrate TPP.cm
  >cmsearch -g TPP.cm /db/refseq24/fragment/1.fna > hits.1.txt
 >cat hits.* > hits.txt
 >cmsearch_reformat.pl -T 10 -b scores.tab hits.txt hits.fna
Line: 79 to 78
  >genomic_context.pl -b scores.tab -d /db/index/refseq24 hits.sto context
Especially note the additional cmcalibrate step which accelerates the cmsearch.
META FILEATTACHMENT attachment="riboswitch_methods.tar.gz" attr="h" comment="" date="1245552342" name="riboswitch_methods.tar.gz" path="riboswitch_methods.tar.gz" size="1541965" stream="riboswitch_methods.tar.gz" tmpFilename="/usr/tmp/CGItemp58033" user="JeffreyBarrick" version="1"
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