FramePlot (Ishikawa & Hotta, 1999)

Genes of bacteria which have a high G+C content genome DNA such as Streptomyces possess biased codon usage. This results in extremely high G+C distribution at the third-letter of each codon. Streptomyces genes actually have an average third-letter G+C content of 92%, which was calculated from 2,008 Streptomyces genes recorded in the CUTG database (Nakamura et al., 1998) based on the GenBank database release 108. This characteristic enables the prediction of protein-coding region in such bacteria. The Frame analysis was first developed by Bibb et al. (1984), and it is one of the essential analyses for studying Streptomyces genetics even at the present time

Sample Results

• Streptomyces griseus kan gene encoding aminoglycoside 3-N-acetyltransferase
• Mycobacterium bovis genes for 32kDa protein (antigen 85 A) and MPB51, complete cds
• Pseudomonas aeruginosa uvrB gene
• Micrococcus luteus Rho factor (rho) gene, complete cds

Functions

Main page

DNA sequence:

Enter your DNA sequence. Don't include comments. Digits and spaces are ignored. The program substitutes T for U.

Window size (default = 40 codons):

Choose the size of sliding window.

Start codon (default = ATG):

Choose the codon(s) recognized as start codon.

Step Size (default = 5 codons):

Window is moved along the sequence by the chosen step size. Larger step size makes the program run much faster. It will produce low resolution plot, but using of the default value gives a satisfactory result in nine cases out of ten.

Minimum ORF size (default = 20 codons):

The program recognizes ORFs which are larger than minimum ORF size as ORF.

Incomplete ORF (default ON)

The program recognizes incomplete ORFs which don't have apparent start or stop codon.

Image width (default = auto):

Choose the width of the output image. By default, Image width is adjusted automatically.

Image color (default = color):

Choose the color of the output image (color or black/white).

Sequence label:

Specify a description for the sequence. This does not affect the result.

Result page

Clickable Map:

You can get nucleotide and amino acid sequence (FASTA format) of the ORF you interested by clicking on the graph. Translation is performed as following manner:

1           2        3      E
>---100aa--->--50aa-->-10aa-|
     A          B       C                   

• clicking on A yields translation from the start codon 1.
• clicking on B yields translation from the start codon 2.
• clicking on C yields translation from the start codon 2 too. That is because the ORF (3 to E) is smaller, by default, than minimum ORF size.

Features page

BLAST Gateway:

You can submit the sequence immediately to the NCBI BLAST server by clicking of [Submit] button.

References

Bibb, M.J., Findlay, P.R. and Johnson, M.W. (1984)

The relationship between base composition and codonusage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30: 157-166.

Ishikawa, J. and Hotta, K. (1991)

Nucleotide sequence and transcriptional start point of the kan gene encoding an aminoglycoside 3-N-acetyltransferase from Streptomyces griseus SS-1198PR. Gene 108: 127-132.

Ishikawa, J. and Hotta, K. (1999)

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.

Nakamura, Y., Gojobori, T. and Ikemura, T. (1998)

Codon usage tabulated from the international DNA sequence databases. Nucl. Acids Res. 26:334.