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News
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| Version 4.0beta is out! (for longer sequence; fully Ajaxified!)
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Try CUPlot 1.0,
which helps identification of CDSs by using codon usage instead of third-letter G+C.
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[Citation]
Ishikawa, J. and Hotta, K.
FEMS Microbiol. Lett. 174:251-253 (1999).
(PubMed)
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Please Try!!!
2ndFind
is a web-based support tool to find
secondary metabolite biosynthetic gene cluster.
It is suitable for analyzing
"contig" sequence.
$Date: 2002/06/11 11:05:43 $
(c) 1996-2002, ISHIKAWA Jun
CAUTION:
No warranty! ``USE AT YOUR OWN RISK''.
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
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-
Papers cited FramePlot |
Papers NOT cited FramePlot
- 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.