Difference: SupplementRiboswitchPrediction (2 vs. 3)

Revision 32009-06-21 - JeffreyBarrick

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META TOPICPARENT name="SupplementList"

Predicting Riboswitch Regulation on a Genomic Scale

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 >fragment_db.pl -s 40 /db/refseq24/fasta /db/refseq24/fragment
 >cmbuild TPP.cm TPP.sto
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 >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
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  >genomic_context.pl -b scores.tab -d /db/index/refseq24 hits.sto context
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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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