50KB_TestPattern

AminoSee DNA Render Summary for /home/tom/Sites/AminoSee/dna/50KB_TestPattern.txt Science render mode

M3C1H3.3

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

255,128,128

13,617 Composite of all amino acids 50KB_TestPattern Reference
1. Ochre

255,128,128

1,401 STOP Codon 50KB_TestPattern Ochre
2. Glutamic acid

16°

255,162,128

274 Group III: Acidic amino acids 50KB_TestPattern Glutamic acid
3. Aspartic acid

31°

255,193,128

274 Group III: Acidic amino acids 50KB_TestPattern Aspartic acid
4. Amber

47°

255,227,128

777 STOP Codon 50KB_TestPattern Amber
5. Cysteine

63°

249,255,128

274 Group II: Polar, uncharged amino acids 50KB_TestPattern Cysteine
6. Glycine

78°

217,255,128

548 Group I: Nonpolar amino acids 50KB_TestPattern Glycine
7. Alanine

94°

183,255,128

548 Group I: Nonpolar amino acids 50KB_TestPattern Alanine
8. Methionine

110°

149,255,128

1,385 START Codon 50KB_TestPattern Methionine
9. Valine

125°

128,255,138

548 Group I: Nonpolar amino acids 50KB_TestPattern Valine
10. Leucine

141°

128,255,172

959 Group I: Nonpolar amino acids 50KB_TestPattern Leucine
11. Isoleucine

157°

128,255,206

411 Group I: Nonpolar amino acids 50KB_TestPattern Isoleucine
12. Phenylalanine

172°

128,255,238

274 Group I: Nonpolar amino acids 50KB_TestPattern Phenylalanine
13. Tryptophan

188°

128,238,255

137 Group I: Nonpolar amino acids 50KB_TestPattern Tryptophan
14. Serine

203°

128,206,255

822 Group II: Polar, uncharged amino acids 50KB_TestPattern Serine
15. Threonine

219°

128,172,255

548 Group II: Polar, uncharged amino acids 50KB_TestPattern Threonine
16. Opal

240°

128,128,255

1,697 STOP Codon 50KB_TestPattern Opal
17. Glutamine

250°

149,128,255

274 Group II: Polar, uncharged amino acids 50KB_TestPattern Glutamine
18. Asparagine

266°

183,128,255

274 Group II: Polar, uncharged amino acids 50KB_TestPattern Asparagine
19. Tyrosine

282°

217,128,255

274 Group II: Polar, uncharged amino acids 50KB_TestPattern Tyrosine
20. Arginine

297°

249,128,255

822 Group IV: Basic amino acids 50KB_TestPattern Arginine
21. Lysine

313°

255,128,227

274 Group IV: Basic amino acids 50KB_TestPattern Lysine
22. Histidine

329°

255,128,193

274 Group IV: Basic amino acids 50KB_TestPattern Histidine
23. Proline

344°

255,128,162

548 Group I: Nonpolar amino acids 50KB_TestPattern Proline
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

1D Linear Map Image

2D Hilbert Map Image

Render Summary

          
Canonical Name: 50KB_TestPattern
Canonical PNG: 50KB_TestPattern.txt_linear_c1_sqr_sci.png
Source: 50KB_TestPattern.txt
Full path: /home/tom/Sites/AminoSee/dna/50KB_TestPattern.txt
Started: 1:11:49 pm Finished: 1:11:50 pm Used: 1.262 seconds  
Machine load averages: 7.43 / 7.4 / 7.27
Bandwidth: 31.25KB / sec DNA Filesize: 48.83KB
Image Output bytes: 53.19KB
Pixels (linear): 13,617 Image aspect Ratio: sqr
Pixels (hilbert): 4,096 (auto) Dimension 3 Hilbert curve
Linear to Hilbert reduction: 3.32 Oversampling: 4
Custom flags: F-C_autoK------M3 C1-INaN "Science mode" render style
Estimated Codons: 16,668 (filesize % 3)
Actual Codons matched: 13,617  
Estimate accuracy: 122% of actual 
Non-coding characters: 16
Coding characters: 40,875
Codons per pixel: 1 (linear) 3.32 (hilbert projection)
Max pix setting: NaN
Darken Factor 0.25 / Highlight Factor 4 Black Point: 128
301 Gigabytes processed on cheese:
Render serial: 1,287 Render UID: 1568855510546
AminoSee version: 1.28.1
          

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DNA/RNA Chromosome Viewer

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



Hilbert Projection

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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.