On the utility of alternative amino acid scripts

Darren R. Flower

Research output: Contribution to journalArticlepeer-review


In this work we propose the hypothesis that replacing the current system of representing the chemical entities known as amino acids using Latin letters with one of several possible alternative symbolic representations will bring significant benefits to the human construction, modification, and analysis of multiple protein sequence alignments. We propose ways in which this might be done without prescribing the choice of actual scripts used. Specifically we propose and explore three ways to encode amino acid texts using novel symbolic alphabets free from precedents. Primary orthographic encoding is the direct substitution of a new alphabet for the standard, Latin-based amino acid code. Secondary encoding imposes static residue groupings onto the orthography of the alphabet by manipulating the shape and/or orientation of amino acid symbols. Tertiary encoding renders each residue as a composite symbol; each such symbol thus representing several alternative amino acid groupings simultaneously. We also propose that the use of a new group-focussed alphabet will free the colouring of amino acid residues often used as a tool to facilitate the representation or construction of multiple alignments for other purposes, possibly to indicate dynamic properties of an alignment such as position-wise residue conservation.
Original languageEnglish
Pages (from-to)539-542
Number of pages4
Issue number12
Publication statusPublished - 28 Jun 2012

Bibliographical note

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.


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