FramePlot
FramePlot is an implementation of the Frame analysis, which is the
method for predicting protein-coding region of bacterial DNA with high
G+C content.
Reference:
Bibb, M.J., et al. Gene 30: 157-66 (1984).
Latest release version
(is believed to be stable:-)
Source code is provided ``AS IS''.
GD.pm patch is also available.
Development version with new feature.
Very unstable!
Sample Results
Gallery
Stats.
1998
1997
Citation
-
Ishikawa, J. and Hotta, K.
- FramePlot: a new implementation of the Frame analysis
for predicting protein-coding regions in bacterial DNA with
a high G+C content.
FEMS Microbiol. Lett. 174:251-253 (1999)
Change history
- Version 2.3 (1999/6/20):
- ORF table with RADIO button.
FEATURES in new window.
Improved ORF-drawing routine.
"S" treated as "G/C".
- Version 2.2.1 (1999/1/13):
- bug fix.
- Version 2.2 (1999/1/11):
- Set max. imagewidth to 7000.
Recognizing incomplete ORF (default ON).
- Version 2.1 (1998/4/26):
- Black & white mode by using of
fly v.1.6.0
- Version 2.0 (1998/2/27):
- Clickable map (really great!).
Gateway to the NCBI BLAST server.
Step size option (fast analysis).
Recognizing CTG as a start codon.
Auto image width.
Rewrote indexing loops.
- Version 1.2 (1997/6/15):
- Changed the way of selecting start codon.
Recognizing ATT as a start codon.
- Version 1.1 (1997/6/10):
- Added complementary strand analysis function.
Improved average G+C% routine.
Improved 3rd-letter G+C% routine (30% speed up).
- Version 1.0 (1997/3/17):
- Replaced \$cgipath with \$ENV{'SCRIPT_NAME'}
- Version 0.7 (1997/1/22):
- Listing open reading frame.
Added minimum ORF size option.
Fixed ATTG bug.
- Version 0.6 (1996/12/28):
- Recognizing both ATG and GTG as start codons.
Showing open reading frame.
- Version 0.5 (1996/12/15):
- Recognizing (A)TTG as a start codon.
Changed internal data structure (about 2-fold faster).
- Version 0.4 (1996/12/13):
- Improved start/stop codon searching routine
(over 100-fold faster than the original).
- Version 0.3 (1996/12/10):
- Recognizing GTG as a start codon.
20-30% faster than version 0.2 (Is that true?:-).
Interlaced GIF.
- Version 0.2 (1996/12/9):
- Added data removing function,
START/STOP codon table,
sequence label option,
and image width option.
- Version 0.1 (1996/12/8):
- initial release.
Only recognizes "ATG" as start codon.
Not available complementary strand analysis.
To Do
- speed up!
- presentation quality plot
- e-mail reply
- graph re-drawing
- command-line use
Acknowledgments
I thank Dr. H. Ikeda for critical comments.
I give special thanks to Dr. M.J. Bibb,
who has first developed the Frame analysis,
and the Streptomyces-mailing list members
for encouraging comments.
Graph plotting done with
Fly,
by Martin Gleeson.
Last modified: Thu Jun 24 14:39:13 1999