Amino acid sequence converter

Each PropertyName must be enclosed in single quotation marks and is case insensitive. GeneticCodeValue can be an integer, character vector, or string specifying a code number or code name from the table Genetic Code.

The amino acid to nucleotide codon mapping for the Standard genetic code is shown in the table Standard Genetic Code. Default is 'DNA'. Choose a web site to get translated content where available and see local events and offers. Based on your location, we recommend that you select:. Select the China site in Chinese or English for best site performance.

Other MathWorks country sites are not optimized for visits from your location. Get trial now. Toggle Main Navigation. Open Mobile Search. One way to improve the musicality is to express each amino acid as a chord, rather than a single note. We then devised a reduced note range using chords, in which similar amino acids were paired initially.

Thus, aspartic acid and glutamic acid were paired, as were leucine and isoleucine, tyrosine and phenylalanine, valine and alanine, threonine and serine, glutamine and asparagine, and arginine and lysine. The paired amino acids were assigned the same fundamental single note, but distinguished by being given a different version of their respective chord. For example, tyrosine and phenylalanine are both assigned a G major chord. The paired amino acids are distinguished from each other by either being assigned to a root position or first inversion chord of the same key signature.

Tyrosine is assigned a G major root position RP chord and phenylalanine is assigned to a G major first inversion FI chord. The initial 13 base notes, assigned roughly according to hydrophobicity, yielded the music for ThyA shown in Figure 1b see legend. Although the complete range of notes included in the chords spans more than 13 notes, the use of triads modulates the sound of the large jumps and range in addition to increasing the complexity of the music. Human thymidylate synthase A ThyA protein sequence converted into single notes based on a note range.

Having a one-to-one ratio of amino-acid assignment to musical notes results in a range that spans 2. Though this code may initially be the most obvious assignment, the approach leaves large jumps between consecutive notes as pointed out by the arrows. The large intervals occur sporadically and tend to interrupt any cohesive melody that may be heard.

The note range assignment also limits musicality and the ability to create a memorable theme. Certain similar amino acids were paired and assigned a three-note chord triad starting an octave below middle C.

Each member of the amino-acid pair was distinguished from the other by using different variations of the same fundamental triad, namely the root position RP and first inversion FI chord.

The result is a reduced, base note range that minimizes the interval jumps between consecutive notes and produces a fuller sound with the use of the triads based on a particular key signature. For example, tyrosine is represented by a G major, root position triad. The next step was to add rhythm, which we did by referring to the coding sequence shown for humans and assigning one of four note durations to each amino-acid codon based on the codon usage frequency per 1, occurrences.

The more abundant the codon is for a particular organism, the longer the note duration. One can see the new rhythmic adjustments in Figure 2a , where the reduced note range assignment is used for the human ThyA protein.

The resulting music addresses the issues of musicality such as large interval jumps and rhythm, which makes the musical translation more pleasing to listen to and maintains the integrity of the protein sequence within the music.

Figure 2b illustrates the difference that can be recognized when various protein motifs are scored. Here, we transposed the beginning segment of the huntingtin protein involved in Huntington's disease [ 11 ]. A clear auditory pattern emanates from both repetitive glutamines 21 in this normal individual and polyproline stretches. The repeated notes are distinctly set apart from the rest of the sequence, allowing one to recognize this region by ear.

Partial human ThyA protein sequence with rhythm based on the human codon distribution. Zero to 10 per 1, was assigned the eighth note, 11 to 20 the quarter note, 21 to 30 a half note, and a codon usage greater than 30 was assigned the whole note. The more frequently a particular codon is used, the longer the note length that represents such a codon. The wild-type huntingtin protein contains 21 glutamines in the beginning portion of the sequence. The protein also contains proline-rich regions.

The repetition in these regions can be distinctly heard in the musical translation. By converting genomic sequences into music, we hope to achieve several goals, which include investigating sequences by the vision impaired. Another aim is to attract young people into molecular genetics by using the multidisciplinary approach of fusing music and science.

There are strong associations between music and perception. Heightened interest in a historically known condition called synesthesia or synaesthesia has also spanned multiple fields of study including science, music, and history [ 12 ]. The condition has prompted a collaborative approach among various disciplines aimed at developing a more comprehensive picture of this syndrome.

Synesthesia is an involuntary perception produced by stimulation of another sense. Commonly one hears a certain pitch that consistently evokes a particular color. Synesthesia is considered an unusually strong cross-modal association in the brain and has been observed in children and adults [ 12 ]. Another example of a collaborative, cross-disciplinary effort includes research pertaining to sound-induced photisms. Sound-induced photisms have been recorded where a startled reaction to a sound soft or loud evokes colors ranging from flashes of white light to a colorful flame [ 13 ].

A separate study confirms that lighter colors 'fit together' with higher pitches of sound and darker stimuli are better fitted to lower pitches [ 14 ]. In future studies, we will use a recently created program F. Pettit, unpublished work , now in its testing stages, which implements the translation rules we have formulated.

Use of this program will enable very rapid translation of large segments of genomes into music. Choose a web site to get translated content where available and see local events and offers. Based on your location, we recommend that you select:. Select the China site in Chinese or English for best site performance. Other MathWorks country sites are not optimized for visits from your location.

Get trial now. Toggle Main Navigation. Search MathWorks. Open Mobile Search. Off-Canvas Navigation Menu Toggle. Main Content. Input Arguments SeqAA One of the following: Character vector or string of single-letter codes specifying an amino acid sequence.

Tip If you use a code name, you can truncate the name to the first two letters of the name. Examples collapse all Convert an amino acid sequence to a nucleotide sequence.