Caenorhabditisel.dna_sm.toplevel

AminoSee DNA Render Summary for /home/tom/Sites/AminoSee/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa Science render mode

M5C37H510.1

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

255,128,128

33,428,798 Composite of all amino acids Caenorhabditisel.dna_sm.toplevel Reference
1. Ochre

255,128,128

728,847 STOP Codon Caenorhabditisel.dna_sm.toplevel Ochre
2. Glutamic acid

16°

255,162,128

1,278,808 Group III: Acidic amino acids Caenorhabditisel.dna_sm.toplevel Glutamic acid
3. Aspartic acid

31°

255,193,128

802,003 Group III: Acidic amino acids Caenorhabditisel.dna_sm.toplevel Aspartic acid
4. Amber

47°

255,227,128

350,727 STOP Codon Caenorhabditisel.dna_sm.toplevel Amber
5. Cysteine

63°

249,255,128

947,314 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Cysteine
6. Glycine

78°

217,255,128

1,116,059 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Glycine
7. Alanine

94°

183,255,128

1,116,319 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Alanine
8. Methionine

110°

149,255,128

528,326 START Codon Caenorhabditisel.dna_sm.toplevel Methionine
9. Valine

125°

128,255,138

1,613,654 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Valine
10. Leucine

141°

128,255,172

3,226,761 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Leucine
11. Isoleucine

157°

128,255,206

2,430,383 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Isoleucine
12. Phenylalanine

172°

128,255,238

2,986,319 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Phenylalanine
13. Tryptophan

188°

128,238,255

411,280 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Tryptophan
14. Serine

203°

128,206,255

2,893,966 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Serine
15. Threonine

219°

128,172,255

1,615,660 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Threonine
16. Opal

240°

128,128,255

707,395 STOP Codon Caenorhabditisel.dna_sm.toplevel Opal
17. Glutamine

250°

149,128,255

1,185,774 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Glutamine
18. Asparagine

266°

183,128,255

1,850,991 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Asparagine
19. Tyrosine

282°

217,128,255

1,040,068 Group II: Polar, uncharged amino acids Caenorhabditisel.dna_sm.toplevel Tyrosine
20. Arginine

297°

249,128,255

1,920,505 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Arginine
21. Lysine

313°

255,128,227

2,672,335 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Lysine
22. Histidine

329°

255,128,193

881,787 Group IV: Basic amino acids Caenorhabditisel.dna_sm.toplevel Histidine
23. Proline

344°

255,128,162

1,123,517 Group I: Nonpolar amino acids Caenorhabditisel.dna_sm.toplevel Proline
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

1D Linear Map Image

2D Hilbert Map Image

Render Summary

          
Canonical Name: Caenorhabditisel.dna_sm.toplevel
Canonical PNG: Caenorhabditisel.dna_sm.toplevel.fa_linear_c37_fix_sci.png
Source: Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa
Full path: /home/tom/Sites/AminoSee/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa
Started: 1:37:47 am Finished: 1:46:47 am Used: 8 minutes, 56.065 seconds  
Machine load averages: 16.08 / 15.53 / 11.64
Bandwidth: 182.62KB / sec DNA Filesize: 97.23MB
Image Output bytes: 3.45MB
Pixels (linear): 903,481 Image aspect Ratio: fix
Pixels (hilbert): 65,536 (auto) Dimension 5 Hilbert curve
Linear to Hilbert reduction: 13.79 Oversampling: 4
Custom flags: --C_autoK------M5 C37-I1000000 "Science mode" render style
Estimated Codons: 33,986,093 (filesize % 3)
Actual Codons matched: 33,428,798  
Estimate accuracy: 102% of actual 
Non-coding characters: 401
Coding characters: 100,286,841
Codons per pixel: 37 (linear) 510.08 (hilbert projection)
Max pix setting: 1,000,000
Darken Factor 0.25 / Highlight Factor 4 Black Point: 128
286.4 Gigabytes processed on cheese:
Render serial: 1,267 Render UID: 1568813867462
AminoSee version: 1.28.1
          

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Linear Projection

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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.