TransTermHP

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An RNA motif tool used to locate Rho-independent transcription terminators in bacterial genomes. Originally name TransTerm while developed at TIGR [1], TransTermHP is currently being rewritten from scratch by Steven Salzberg's lab.

The newest version can be found here.

Raw TransTermHP Output

This is a portion of output from a TransTermHP search of the Bacillus subtilis genome.

 TransTermHP v2.04 (Nov  9 2006)
 25 bins; sample size is 20000000
 --pval-conf=/Users/cjfields/bin/expterm.dat
 
 --gc=-2.3 --au=-0.9 --gu=1.3 --mm=3.5 --gap=6
 --max-len=59 --min-stem=4 --max-loop=13 --min-loop=3
 --uwin-length=6 --uwin-require=3 --max-hp-score=-2 --max-tail-score=-2.5
 --loop-penalty=1,2,3,4,5,6,7,8,9,10,11
 --start-cut=0 --end-cut=25
 
 Genes: 0.555347 %AT, 3572429 nt, 23269 terms.
 Intergenic: 0.617508 %AT, H2T: 460878 nt, 3344 terms; T2T: 104940 nt, 2636 terms; H2H: 177875 nt, 2468 terms. 
 
 Each terminator entry starts in column 3 and is of the form:
   term #       start - end      +/-  regionconf   hp     tail | notes
 Followed by the sequence of the 5' tail, 5' stem, loop, 3' stem, and 3' tail.
 Genes are interspersed, and start the first column.
 
 
 SEQUENCE gi|50812173|ref|NC_000964.2| Bacillus subtilis subsp. subtilis str. 168, complete genome (length 4214630)
 
 dnaA              410 - 1750     + | chromosomal replication initiation protein
   TERM 1         1802 - 1831     + F   100 -13.7 -4.02999 | opp_overlap 1777 1800 1804 1806, overlap 1793
   TTTTCGGAAGTCATA       CACAGTCTGTCCA CATG TGGATAGGCTGTG        TTTCCTGTCTTTTTC
 dnaN             1939 - 3075     + | DNA polymerase III subunit beta
   TERM 2         3087 - 3106     + F   100 -13.6 -4.69326 | opp_overlap 3085
   TTAATCCGATACACT            GCTGCCGA CCCG TCGGCAGC             TTTTCTATTCGGTAT
 yaaA             3206 - 3421     + | hypothetical protein
 recF             3437 - 4549     + | recombination protein F
 yaaB             4567 - 4725     + | hypothetical protein
 gyrB             4866 - 6782     + | DNA topoisomerase IV subunit B
   TERM 3         6792 - 6817     + F   100 -10.6 -5.24129 | opp_overlap 6792 6808
   ATCTAATCATAAAAA         GCCTTATTTC CAATAA GAAATAAGGC          TTTTTTCTGAACAAG
 .....

References

  1. Ermolaeva MD, Khalak HG, White O, Smith HO, and Salzberg SL. Prediction of transcription terminators in bacterial genomes. J Mol Biol. 2000 Aug 4;301(1):27-33. DOI:10.1006/jmbi.2000.3836 | PubMed ID:10926490 | HubMed [transterm]
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