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 |