TransTermHP
From BioPerl
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 .....
