megabase

AminoSee DNA Render Summary for /home/tom/Sites/AminoSee/dna/megabase.fa Science render mode

M5C4H5

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

255,128,128

324,599 Composite of all amino acids megabase Reference
1. Ochre

255,128,128

5,697 STOP Codon megabase Ochre
2. Glutamic acid

16°

255,162,128

12,169 Group III: Acidic amino acids megabase Glutamic acid
3. Aspartic acid

31°

255,193,128

7,458 Group III: Acidic amino acids megabase Aspartic acid
4. Amber

47°

255,227,128

3,443 STOP Codon megabase Amber
5. Cysteine

63°

249,255,128

12,308 Group II: Polar, uncharged amino acids megabase Cysteine
6. Glycine

78°

217,255,128

19,304 Group I: Nonpolar amino acids megabase Glycine
7. Alanine

94°

183,255,128

15,884 Group I: Nonpolar amino acids megabase Alanine
8. Methionine

110°

149,255,128

6,005 START Codon megabase Methionine
9. Valine

125°

128,255,138

17,264 Group I: Nonpolar amino acids megabase Valine
10. Leucine

141°

128,255,172

33,907 Group I: Nonpolar amino acids megabase Leucine
11. Isoleucine

157°

128,255,206

16,584 Group I: Nonpolar amino acids megabase Isoleucine
12. Phenylalanine

172°

128,255,238

16,850 Group I: Nonpolar amino acids megabase Phenylalanine
13. Tryptophan

188°

128,238,255

6,262 Group I: Nonpolar amino acids megabase Tryptophan
14. Serine

203°

128,206,255

28,959 Group II: Polar, uncharged amino acids megabase Serine
15. Threonine

219°

128,172,255

17,333 Group II: Polar, uncharged amino acids megabase Threonine
16. Opal

240°

128,128,255

6,274 STOP Codon megabase Opal
17. Glutamine

250°

149,128,255

12,988 Group II: Polar, uncharged amino acids megabase Glutamine
18. Asparagine

266°

183,128,255

11,616 Group II: Polar, uncharged amino acids megabase Asparagine
19. Tyrosine

282°

217,128,255

8,528 Group II: Polar, uncharged amino acids megabase Tyrosine
20. Arginine

297°

249,128,255

18,452 Group IV: Basic amino acids megabase Arginine
21. Lysine

313°

255,128,227

16,911 Group IV: Basic amino acids megabase Lysine
22. Histidine

329°

255,128,193

11,792 Group IV: Basic amino acids megabase Histidine
23. Proline

344°

255,128,162

18,611 Group I: Nonpolar amino acids megabase Proline
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

1D Linear Map Image

2D Hilbert Map Image

Render Summary

          
Canonical Name: megabase
Canonical PNG: megabase.fa_linear_c4_fix_sci.png
Source: megabase.fa
Full path: /home/tom/Sites/AminoSee/dna/megabase.fa
Started: 2:24:06 am Finished: 2:24:10 am Used: 2.918 seconds  
Machine load averages: 9.39 / 9.74 / 10.5
Bandwidth: 331.05KB / sec DNA Filesize: 978.54KB
Image Output bytes: 316.99KB
Pixels (linear): 81,149 Image aspect Ratio: fix
Pixels (hilbert): 65,536 (auto) Dimension 5 Hilbert curve
Linear to Hilbert reduction: 1.24 Oversampling: 4
Custom flags: --C_autoK------M5 C4-I1000000 "Science mode" render style
Estimated Codons: 334,008 (filesize % 3)
Actual Codons matched: 324,599  
Estimate accuracy: 103% of actual 
Non-coding characters: 0
Coding characters: 987,910
Codons per pixel: 4 (linear) 4.95 (hilbert projection)
Max pix setting: 1,000,000
Darken Factor 0.25 / Highlight Factor 4 Black Point: 128
287.4 Gigabytes processed on cheese:
Render serial: 1,275 Render UID: 1568816647174
AminoSee version: 1.28.1
          

AminoSeeNoEvil

DNA/RNA Chromosome Viewer

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



Hilbert Projection

This is a curve that touches each pixel exactly once, without crossing over or breaking.

Linear Projection

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

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.