AminoSee DNA Render Summary for Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa

Caenorhabditisel.dna_sm.toplevel

Reference image - all amino acids blended togetherAmberTryptophanMethionineOpalOchreAspartic acidHistidineCysteineTyrosineGlycineAlanineProlineGlutamineGlutamic acidValineThreonineAsparagineArginineIsoleucineLysineSerinePhenylalanineLeucine
  
    Canonical Filename: Caenorhabditisel.dna_sm.toplevel
    Source: Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa
    Run ID: 1557448213 Host: cheese
    AminoSee version: 1.7.3
    Highlight set: false none
    Highlights: none
    Your custom flags: FD      
    Science Mode
    Aspect Ratio: fix
    Input bytes: 101,958,278
    Output bytes: 4,194,304
    Estimated Codons by file size: 33,986,093
    Actual Codons matched: 33,428,798
    Estimate accuracy: 2%
    Non-Base Clock: 401
    Bases Clock: 100,286,841
    Codons per pixel linear image: 3.78
    Codons per pixel hilbert: 30.1
    Pixels linear: 8,357,199
    Pixels hilbert: 1,048,576
    Scale down factor:  7.97
    overSampleFactor: 3
    Amino acid blend opacity: 26.48%
    Users Max magnitude: 7/ 10  Max pix:9,000,000
    Hilbert Magnitude: 7 / 7
    Hilbert Curve Pixels: 1048576
    Darken Factor 1
    Highlight Factor 2.89
    Time used: 80,046 miliseconds
  

1D Linear Map Image

2D Hilbert Map Image

AminoSeeNoEvil

DNA/RNA Chromosome Viewer

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



Amino Acid Hue RGB Count Description Hilbert PNG
All amino acids combined =

n/a

n/a

33428798 n/a Reference Image Caenorhabditisel.dna_sm.toplevel
Non-coding NNN

120°

128,255,128

0 Expressed as NNN Codon Non-coding_NNN
Start Codons

120°

128,255,128

0 Count of Methionine Start_Codons
Stop Codons

120°

128,255,128

0 One of Opal, Ochre, or Amber Stop_Codons
Amber

47°

255,227,128

350,727 STOP Codon Amber
Tryptophan

188°

128,238,255

411,280 Group I: Nonpolar amino acids Tryptophan
Methionine

110°

149,255,128

528,326 START Codon Methionine
Opal

240°

128,128,255

707,395 STOP Codon Opal
Ochre

255,128,128

728,847 STOP Codon Ochre
Aspartic acid

31°

255,193,128

802,003 Group III: Acidic amino acids Aspartic_acid
Histidine

329°

255,128,193

881,787 Group IV: Basic amino acids Histidine
Cysteine

63°

249,255,128

947,314 Group II: Polar, uncharged amino acids Cysteine
Tyrosine

282°

217,128,255

1,040,068 Group II: Polar, uncharged amino acids Tyrosine
Glycine

78°

217,255,128

1,116,059 Group I: Nonpolar amino acids Glycine
Alanine

94°

183,255,128

1,116,319 Group I: Nonpolar amino acids Alanine
Proline

344°

255,128,162

1,123,517 Group I: Nonpolar amino acids Proline
Glutamine

250°

149,128,255

1,185,774 Group II: Polar, uncharged amino acids Glutamine
Glutamic acid

16°

255,162,128

1,278,808 Group III: Acidic amino acids Glutamic_acid
Valine

125°

128,255,138

1,613,654 Group I: Nonpolar amino acids Valine
Threonine

219°

128,172,255

1,615,660 Group II: Polar, uncharged amino acids Threonine
Asparagine

266°

183,128,255

1,850,991 Group II: Polar, uncharged amino acids Asparagine
Arginine

297°

249,128,255

1,920,505 Group IV: Basic amino acids Arginine
Isoleucine

157°

128,255,206

2,430,383 Group I: Nonpolar amino acids Isoleucine
Lysine

313°

255,128,227

2,672,335 Group IV: Basic amino acids Lysine
Serine

203°

128,206,255

2,893,966 Group II: Polar, uncharged amino acids Serine
Phenylalanine

172°

128,255,238

2,986,319 Group I: Nonpolar amino acids Phenylalanine
Leucine

141°

128,255,172

3,226,761 Group I: Nonpolar amino acids Leucine
19 Amino Acids, 4 Start/Stop codes, 1 NNN . . . .

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 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: