FindTerm - a program for searching bacterial terminators in DNA sequences. The set of conditions for searching bacterial terminators is stored in the config file.

Scheme of transcription

This scheme corresponds to positive direction (+) of tranccription form 3' to 5' end of DNA, and when we search terminators oriented from 5' to 3' end, found structure will be marked by (-) in the output file (see below).

First the program searches for region, which meets the requirements for T-reach region. Then it tries possible combinations of spacer lengths. At last, it finds all hairpins which meet user-defined parameters and complementarity rules. Then it searches the next appropriate T-reach region. Structures which meet all requirements are displayed.

Output and representing the results
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There are examples of FindTerm output:

FindTerm - search for Rho-independent bacterial terminators
(Softberry, 2004)
Mode: All non-overlapping
Chain Start Length   Score
  -       2     33   -22.9
  +      93     53   -33.1
  -     210     52   -33.3
  +     315     53   -37.5
  +     423     53   -24.8

or

FindTerm - search for Rho-independent bacterial terminators
(Softberry, 2004)
Mode: Best terminator
Chain Start Length   Score
  +     423     53   -37.5


<Chain>  indicates the chain direction:
         (+) means that terminator is oriented from 3' to 5' end of DNA
         (-) means that terminator is oriented from 5' to 3' end of DNA
<Start>  is the position at which terminator begins
<Length> is the length of terminator, from the start of hairpin and up to end of T-reach region
<Score>  is the value of score function, including enegy of terminator. 
         The lower Score corresponds to the better terminator.

Program is provided with viewer.