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).

FramePlot-2.3

Latest release version (is believed to be stable:-)
Source code is provided ``AS IS''. GD.pm patch is also available.

FramePlot-3.0beta

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

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