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  FindTerm

FindTerm

FindTerm - a program for searching bacterial terminators in DNA sequences, using the set of conditions, which can be modified by user. They are stored in the config file (FindTerm.cfg) or any other user-defined config file or even without config, from command line.

Method description
First the program searches for region, which meet the requirements for T-reach region. Then it tries possible combinations of spacer lengths. And 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.

Scheme of transcription

        ___ 
       /   \
      |     | hairpin
       \   /
  5'    |-|
  \_    |-|             (+)
    \_  |-|  spacer
      \_|-|  /
           \   U-reach
            \  area    
             -------------- 3'  mRNA
             ||||||||||||||  
 3'------------------------ 5'   DNA
	
	

This scheme corresponds to positive direction (+) of transcription 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).

Outut examples:

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 energy of terminator. 
         The lower Score corresponds to the better terminator.

15-letter code:

1 A A  
2 T T  
3 G G  
4 C C  
5 W A,T Weak
6 S G,C Strong
7 R A,G puRine
8 Y T,C pYrimidine
9 M A,C aMino (+)
10 K T,G Keto (-)
11 B T,G,C not A
12 V A,G,C not T
13 H A,T,C not G
14 D A,T,G not C
15 N A,T,G,C any

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