TransTermHP

An RNA motif tool used to locate Rho-independent transcription terminators in bacterial genomes. Originally name TransTerm while developed at TIGR transterm, 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

<biblio>

1. transterm pmid=10926490

</biblio>