TransTerm

TransTerm finds rho-independent transcription terminators in bacterial genomes. Each terminator is assigned a confidence value that provides an estimate of its probability of being a true terminator.

Installed on the opteron cluster.

Usage

  • Create a script which calls TransTerm with 

    srun perl /biomed/bin/TransTerm -s sequence-file  \
    -c coordinates-file -o output-file [ -g]

    TransTerm requires two input files: one with a genome sequence and another with genome coordinates. See the README file provided by the TransTerm suppliers for details on these files.

    Using -g enables searching for terminators that have gaps in the stem. If you don't need them, don't use -g and the program will run faster.

    For more information, including a a link to the sample input and output files and descriptions of the files, see the README file provided by the TransTerm suppliers.

  • Submit the job file with the srun command.

Other documentation

  • For a description on how the confidence is calculated see : Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial Genomes. J Mol Biol 301, (1), 27-33 (2000)

See also: