Some general information about the graphs can be found in the section called Graphs and Plots. Configuration options for graphs are described in the section called Options For Plots and Graphs in Chapter 5.
This item will turn off all the visible graphs.
This menu item prompts the user for the name of a file which should contain codon usage data in the same format as the data at this web site. If Artemis successfully loads the codon usage file two new plots will be added to the display menu and will be immediately visible. One plot shows the codon scores (in a sliding window) for each of the forward reading frames and the other shows the same thing for the reverse reading frames. [short name: codon_usage]
The graph is calculated using the codon preference statistic from Gribskov et al. (Nucl. Acids Res. 12; 539-549 (1984)).
Here is an example usage file:
UUU 32.2( 48423) UCU 30.5( 45913) UAU 21.8( 32829) UGU 8.9( 13371)
UUC 13.0( 19519) UCC 12.1( 18149) UAC 11.8( 17721) UGC 5.6( 8372)
UUA 26.0( 39138) UCA 17.9( 26850) UAA 1.3( 1944) UGA 0.5( 733)
UUG 24.0( 36134) UCG 8.0( 12055) UAG 0.5( 705) UGG 10.9( 16364)
CUU 25.3( 38015) CCU 21.9( 32964) CAU 16.3( 24577) CGU 16.3( 24495)
CUC 7.3( 10922) CCC 8.4( 12619) CAC 6.4( 9653) CGC 6.2( 9316)
CUA 8.6( 12957) CCA 12.7( 19075) CAA 27.3( 41066) CGA 7.9( 11896)
CUG 6.3( 9503) CCG 4.6( 6910) CAG 10.9( 16457) CGG 3.0( 4487)
AUU 35.0( 52636) ACU 22.9( 34419) AAU 33.9( 51009) AGU 14.7( 22108)
AUC 12.6( 19000) ACC 10.9( 16378) AAC 17.9( 26895) AGC 9.2( 13905)
AUA 13.1( 19726) ACA 13.9( 20898) AAA 39.3( 59079) AGA 11.1( 16742)
AUG 20.9( 31376) ACG 6.5( 9744) AAG 25.2( 37825) AGG 5.1( 7615)
GUU 29.3( 44015) GCU 30.2( 45397) GAU 38.1( 57240) GGU 22.0( 33101)
GUC 11.0( 16497) GCC 11.6( 17518) GAC 15.8( 23749) GGC 8.5( 12717)
GUA 12.3( 18451) GCA 15.7( 23649) GAA 44.3( 66550) GGA 15.7( 23623)
GUG 8.3( 12422) GCG 5.3( 8011) GAG 21.3( 31979) GGG 4.3( 6497)
Artemis is able to display some types of user data in a graph that looks like the GC content graph (see the section called GC Content (%)). This menu item will prompt the user for the name of a data file which should contain one line per base of sequence and one floating point number per line. Artemis will plot each data point over the corresponding base.
Controls whether the GC content plot is visible. This is a graph of the average GC content of a moving window (default size 120 base), across the bases visible in the overview window. [Default: off] [short name: gc_content]
Controls whether the cutoff GC content plot is visible. This is similar to the GC content graph, but the plot is clipped so that the GC content of each algorithm window is shown only when it is more than 2.5 times the standard deviation of the GC content in all the windows. [Default: off] [short name: sd_gc_content]
Controls whether the AG content plot is visible. This is a graph of the average AG content of a moving window (default size 120 base), across the bases visible in the overview window. [Default: off] [short name: ag_content]
Controls whether the GC frame plot is visible. This graph is similar to the GC content graph but shows the GC content of the first, second and third position independently. For more information on the algorithm and on how to interpret the result see this web page.
See Ishikawa, J. and Hotta, K. FEMS Microbiol. Lett. 174:251-253 (1999) and GC frame plot for more information on the algorithm.
[Default: off] [short name: gc_frame]
Controls whether the (forward) correlation scores plot is visible. The graph shows the correlation between the amino acid composition of the globular proteins in TREMBL and the composition of the base translation in each of the three reading frames. The green line represents forward frame 1, blue represents frame 2 and red represents frame 3. [Default: off] [short name: correlation_score]
This does the same as "Correlation Scores", but does the calculation on the reverse strand. The green line represents reverse frame 1 (the bottom frame line), blue represents frame 2 and red represents frame 3. [Default: off] [short name: correlation_score]
Controls whether the GC deviation plot is visible. This graph shows the difference between the "G" content of the forward strand and the reverse strand.
See "Asymmetric substitution patterns in the two DNA strands of bacteria" Lobry JR. - Mol Biol Evol 1996 May;13(5):660-5.
[Default: off] [short name: gc_deviation]
Controls whether the AT deviation plot is visible. This graph shows the difference between the "A" content of the forward strand and the reverse strand. [Default: off] [short name: at_deviation]
This menu item toggles the display of the graph of the dinucleotide absolute relative abundance difference between the whole sequence and a sliding window.
For details of the algorithm see "Global dinucleotide signatures and analysis of genomic heterogeneity" Samuel Karlin - Current Opinion in Microbiology 1998, 1:598-610.
[Default: off] [short name: karlin_sig]
AT skew is calculated as ([A]-[T])/([A]+[T]), where [A] and [T] are the counts of these bases in the window. Grigoriev A (1999) Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Research 60, 1-19.
Shulman MJ, Steinberg CM, Westmoreland N (1981) The coding function of nucleotide sequences can be discerned by statistical analysis. J Theor Biol 88:409-20.
Konopka Andrzej (1984) Is the information content of DNA evolutionarily significant? J Theor Biol 107:697-704. Informational entropy is calculated from a table of overlapping DNA triplet frequencies, using equation 1 in the above reference. The use of overlapping triplets smooths the frame effect.
Shields DC, Sharp PM (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res 15:8023-40.
Gatherer D, McEwan NR (1997) Small regions of preferential codon usage and their effect on overall codon bias--the case of the plp gene. Biochem Mol Biol Int 43:107-14.
Wright F (1990) The 'effective number of codons' used in a gene. Gene 87:23-9, and Fuglsang A (2004) The 'effective number of codons' revisited. Biochem Biophys Res Commun. May 7;317(3):957-64.
Freire-Picos MA, Gonzalez-Siso MI, Rodriguez-Belmonte E, Rodriguez-Torres AM, Ramil E, Cerdan ME (1994) Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene 139:43-9.