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transtermhp

find rho-independent transcription terminators in bacterial genomes

TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator. TransTermHP is the successor of TransTerm which was using very different search and scoring algorithms.
Homepage:
Package version:2.09-1
Architecture:amd64
Distribution:Ubuntu
Filename:transtermhp_2.09-1_amd64.deb

/usr/share/doc/transtermhp/README.Debian

transtermhp for Debian
----------------------

Helper scripts are located in the /usr/share/doc/transtermhp/examples directory.

 -- Alex Mestiashvili <alex@biotec.tu-dresden.de>  Sat, 19 Feb 2011 12:37:10 +0000

/usr/share/man/man1/2ndscore.1.gz

2NDSCORE(1)        User Contributed Documentation        2NDSCORE(1)



NAME
         2ndscore  - find the best hairpin anchored at each position.

SYNOPSIS
        2ndscore in.fasta > out.hairpins

DESCRIPTION
       For every position in the sequence this will output a line:

          -0.6  52 ..  62      TTCCTAAAGGTTCCA  GCG CAAAA TGC  CATAAGCACCACATT
        (score) (start .. end) (left conte
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/usr/share/man/man1/transterm.1.gz

TRANSTERM(1)       User Contributed Documentation       TRANSTERM(1)



NAME
        transterm  - Finds rho-independent transcription terminators in bacterial genomes.

SYNOPSIS
       transterm -p expterm.dat seq.fasta annotation.ptt > output.tt

DESCRIPTION
       Any number of fasta and annotation files can be listed but
       fasta files should come before annotation files. The type of
      
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/usr/share/doc/transtermhp/RELEASE-NOTES.txt

Version 2.07 (Released on Jan. 21, 2008)
    - Fixed bug that causes -max-loop option to not be reco
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/usr/share/doc/transtermhp/changelog.Debian.gz

transtermhp (2.09-1) unstable; urgency=low

  [ Alex Mestiashvili ]
  * New upstream release. 

  [ 
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/usr/share/doc/transtermhp/copyright

Format: http://dep.debian.net/deps/dep5
Upstream-Name: transterm_hp
Source: http://transterm.cbcb.um
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