News
Version 4.0beta is out! (for longer sequence; fully Ajaxified!) Please try version 3.0beta
Try CUPlot 1.0, which helps identification of CDSs by using codon usage instead of third-letter G+C.
For faster analysis use this URL: http://watson.nih.go.jp/~jun/cgi-bin/frameplot.pl
[Citation] Ishikawa, J. and Hotta, K. FEMS Microbiol. Lett. 174:251-253 (1999). (PubMed)
     Please Try!!!     
2ndFind
is a web-based support tool to find secondary metabolite biosynthetic gene cluster. It is suitable for analyzing "contig" sequence.

FramePlot 2.3.2*

$Date: 2002/06/11 11:05:43 $
(c) 1996-2002, ISHIKAWA Jun
CAUTION: No warranty! ``USE AT YOUR OWN RISK''.

DNA sequence (DON'T include comments. Digits and spaces are ignored.):


This may take a little time to run (200-2000 base/sec depends on option settings).
OPTIONAL PARAMETERS
Window size:
Start codon:
ATG GTG TTG CTG ATT
Step size:
Minimum ORF size:
Incomplete ORF:
Image width:
Image color:
Sequence label (sample#, sequence ID, etc.; optional):

Comments are very much appreciated to: jun@nih.go.jp
Frame analysis predicts protein-coding region of high G+C content bacterial DNA, such as Streptomyces. Brief explanation of the analysis is available ( English / Japanese). Reference: Bibb, M.J., et al. Gene 30: 157-66 (1984).

Sample Results

Miscellaneous information

Change history

Version 2.3.2 (2001/03/09):
Added ``Clear sequence'' button.
Version 2.3.1 (2000/12/16):
Automatic set of ``Sequence label'' for FASTA-formatted data.
Version 2.3 (1999/6/20):
ORF table with RADIO button. FEATURES in a 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.