TransTerm

Dalphin, M. E Stockwell, P. A., Tate, W. P. Brown, C. M. (1999). TransTerm, the translational signal database, extended to include lull coding sequences and untranslated regions. Nucleic Acids Res 27,293-4. 

Identifying Putative Rho-lndependent Terminators Using TransTerm... 

Go to http //www.genomics.jhu.edu/TransTerm/transterm.htmI. If a TransTerm database is available at for the species of interest, copy and paste the published database from Internet Explorer (see Note 2), and save it as a text file. The format of the database should conform to the format of the sample TransTerm database provided in the sRNAPredict2 directory. 

If a TransTerm database is not available for the species of interest, TransTerm can be downloaded at http //www.tufts.edu/sackler/waldorlab/sRNAPredict.htmI and is accompanied by a README file that includes instructions for its installation (see Note 9). 

To run TransTerm, first drag and drop the icon of the TransTerm executable (which is found in the src directory) into the terminal window. 

The TransTerm output file can be used without modification as input in sRNAPredict2 searches. 

After compiling the source code using the make command, go into the TransTerm file (in the src directory) and change the line path = put a path here to a path pointing to the directory in which the file now resides, for example path = /home/bob/favorite programs/TransTerm/src . ... 

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