Chimp_Clint_chrY

AminoSee DNA Render Summary for /home/tom/Sites/AminoSee/dna/Chimp_Clint_chrY.gbk Science render mode

M7C1H7.3

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

255,128,128

7,625,504 Composite of all amino acids Chimp_Clint_chrY Reference
1. Ochre

255,128,128

150,678 STOP Codon Chimp_Clint_chrY Ochre
2. Glutamic acid

16°

255,162,128

279,714 Group III: Acidic amino acids Chimp_Clint_chrY Glutamic acid
3. Aspartic acid

31°

255,193,128

180,349 Group III: Acidic amino acids Chimp_Clint_chrY Aspartic acid
4. Amber

47°

255,227,128

96,306 STOP Codon Chimp_Clint_chrY Amber
5. Cysteine

63°

249,255,128

279,388 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Cysteine
6. Glycine

78°

217,255,128

375,593 Group I: Nonpolar amino acids Chimp_Clint_chrY Glycine
7. Alanine

94°

183,255,128

304,004 Group I: Nonpolar amino acids Chimp_Clint_chrY Alanine
8. Methionine

110°

149,255,128

151,871 START Codon Chimp_Clint_chrY Methionine
9. Valine

125°

128,255,138

394,546 Group I: Nonpolar amino acids Chimp_Clint_chrY Valine
10. Leucine

141°

128,255,172

821,481 Group I: Nonpolar amino acids Chimp_Clint_chrY Leucine
11. Isoleucine

157°

128,255,206

455,418 Group I: Nonpolar amino acids Chimp_Clint_chrY Isoleucine
12. Phenylalanine

172°

128,255,238

449,143 Group I: Nonpolar amino acids Chimp_Clint_chrY Phenylalanine
13. Tryptophan

188°

128,238,255

141,579 Group I: Nonpolar amino acids Chimp_Clint_chrY Tryptophan
14. Serine

203°

128,206,255

680,537 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Serine
15. Threonine

219°

128,172,255

395,263 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Threonine
16. Opal

240°

128,128,255

154,457 STOP Codon Chimp_Clint_chrY Opal
17. Glutamine

250°

149,128,255

306,513 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Glutamine
18. Asparagine

266°

183,128,255

309,911 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Asparagine
19. Tyrosine

282°

217,128,255

242,260 Group II: Polar, uncharged amino acids Chimp_Clint_chrY Tyrosine
20. Arginine

297°

249,128,255

362,334 Group IV: Basic amino acids Chimp_Clint_chrY Arginine
21. Lysine

313°

255,128,227

445,587 Group IV: Basic amino acids Chimp_Clint_chrY Lysine
22. Histidine

329°

255,128,193

271,466 Group IV: Basic amino acids Chimp_Clint_chrY Histidine
23. Proline

344°

255,128,162

377,106 Group I: Nonpolar amino acids Chimp_Clint_chrY Proline
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

1D Linear Map Image

2D Hilbert Map Image

Render Summary

          
Canonical Name: Chimp_Clint_chrY
Canonical PNG: Chimp_Clint_chrY.gbk_linear_c1_fix_sci.png
Source: Chimp_Clint_chrY.gbk
Full path: /home/tom/Sites/AminoSee/dna/Chimp_Clint_chrY.gbk
Started: 5:47:43 am Finished: 5:49:21 am Used: 1 minute, 17.229 seconds  
Machine load averages: 7.04 / 7.06 / 7.08
Bandwidth: 402.34KB / sec DNA Filesize: 30.75MB
Image Output bytes: 29.09MB
Pixels (linear): 7,625,504 Image aspect Ratio: fix
Pixels (hilbert): 1,048,576 (auto) Dimension 7 Hilbert curve
Linear to Hilbert reduction: 7.27 Oversampling: 4
Custom flags: --C_autoK------M7 C1-INaN "Science mode" render style
Estimated Codons: 10,748,435 (filesize % 3)
Actual Codons matched: 7,625,504  
Estimate accuracy: 141% of actual 
Non-coding characters: 6,397,964
Coding characters: 31,822,572
Codons per pixel: 1 (linear) 7.27 (hilbert projection)
Max pix setting: NaN
Darken Factor 0.25 / Highlight Factor 4 Black Point: 128
290.3 Gigabytes processed on cheese:
Render serial: 1,274 Render UID: 1568828863972
AminoSee version: 1.28.1
          

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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.