Kyokai7_BABQ01000000

AminoSee DNA Render Summary for /home/tom/Sites/AminoSee/dna/Kyokai7_BABQ01000000.gff Science render mode

M7C1H4

Amino Acid Hue° RGB Count Description Hilbert PNG
0. Reference

255,128,128

4,150,021 Composite of all amino acids Kyokai7_BABQ01000000 Reference
1. Ochre

255,128,128

90,600 STOP Codon Kyokai7_BABQ01000000 Ochre
2. Glutamic acid

16°

255,162,128

141,472 Group III: Acidic amino acids Kyokai7_BABQ01000000 Glutamic acid
3. Aspartic acid

31°

255,193,128

110,429 Group III: Acidic amino acids Kyokai7_BABQ01000000 Aspartic acid
4. Amber

47°

255,227,128

52,387 STOP Codon Kyokai7_BABQ01000000 Amber
5. Cysteine

63°

249,255,128

120,673 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Cysteine
6. Glycine

78°

217,255,128

155,775 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Glycine
7. Alanine

94°

183,255,128

151,926 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Alanine
8. Methionine

110°

149,255,128

74,787 START Codon Kyokai7_BABQ01000000 Methionine
9. Valine

125°

128,255,138

214,030 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Valine
10. Leucine

141°

128,255,172

428,502 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Leucine
11. Isoleucine

157°

128,255,206

294,721 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Isoleucine
12. Phenylalanine

172°

128,255,238

254,138 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Phenylalanine
13. Tryptophan

188°

128,238,255

60,844 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Tryptophan
14. Serine

203°

128,206,255

361,740 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Serine
15. Threonine

219°

128,172,255

239,446 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Threonine
16. Opal

240°

128,128,255

81,843 STOP Codon Kyokai7_BABQ01000000 Opal
17. Glutamine

250°

149,128,255

145,619 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Glutamine
18. Asparagine

266°

183,128,255

193,069 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Asparagine
19. Tyrosine

282°

217,128,255

159,735 Group II: Polar, uncharged amino acids Kyokai7_BABQ01000000 Tyrosine
20. Arginine

297°

249,128,255

247,040 Group IV: Basic amino acids Kyokai7_BABQ01000000 Arginine
21. Lysine

313°

255,128,227

246,619 Group IV: Basic amino acids Kyokai7_BABQ01000000 Lysine
22. Histidine

329°

255,128,193

150,923 Group IV: Basic amino acids Kyokai7_BABQ01000000 Histidine
23. Proline

344°

255,128,162

173,703 Group I: Nonpolar amino acids Kyokai7_BABQ01000000 Proline
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

1D Linear Map Image

2D Hilbert Map Image

Render Summary

          
Canonical Name: Kyokai7_BABQ01000000
Canonical PNG: Kyokai7_BABQ01000000.gff_linear_c1_fix_sci.png
Source: Kyokai7_BABQ01000000.gff
Full path: /home/tom/Sites/AminoSee/dna/Kyokai7_BABQ01000000.gff
Started: 3:19:13 am Finished: 3:20:19 am Used: 49.842 seconds  
Machine load averages: 10.22 / 10.17 / 10.18
Bandwidth: 316.41KB / sec DNA Filesize: 15.6MB
Image Output bytes: 15.83MB
Pixels (linear): 4,150,021 Image aspect Ratio: fix
Pixels (hilbert): 1,048,576 (auto) Dimension 7 Hilbert curve
Linear to Hilbert reduction: 3.96 Oversampling: 4
Custom flags: -UC_autoK------M7 C1-I4660000 "Science mode" render style
Estimated Codons: 5,451,087 (filesize % 3)
Actual Codons matched: 4,150,021  
Estimate accuracy: 131% of actual 
Non-coding characters: 3,272,793
Coding characters: 16,161,154
Codons per pixel: 1 (linear) 3.96 (hilbert projection)
Max pix setting: 4,660,000
Darken Factor 0.25 / Highlight Factor 4
290.5 Gigabytes processed on cheese:
Render serial: 1,241 Render UID: 1568819954079
AminoSee version: 1.28.0
          

AminoSeeNoEvil

DNA/RNA Chromosome Viewer

A new way to view DNA that attributes a colour hue to each Amino acid codon



About Start and Stop Codons

The codon AUG is called the START codon as it the first codon in the transcribed mRNA that undergoes translation. AUG is the most common START codon and it codes for the amino acid methionine (Met) in eukaryotes and formyl methionine (fMet) in prokaryotes. During protein synthesis, the tRNA recognizes the START codon AUG with the help of some initiation factors and starts translation of mRNA. Some alternative START codons are found in both eukaryotes and prokaryotes. Alternate codons usually code for amino acids other than methionine, but when they act as START codons they code for Met due to the use of a separate initiator tRNA. Non-AUG START codons are rarely found in eukaryotic genomes. Apart from the usual Met codon, mammalian cells can also START translation with the amino acid leucine with the help of a leucyl-tRNA decoding the CUG codon. Mitochondrial genomes use AUA and AUU in humans and GUG and UUG in prokaryotes as alternate START codons. In prokaryotes, E. coli is found to use AUG 83%, GUG 14%, and UUG 3% as START codons. The lacA and lacI coding this.regions in the E coli lac operon don’t have AUG START codon and instead use UUG and GUG as initiation codons respectively.

Linear Projection

The following image is in raster order, top left to bottom right: