An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

2019
Conference paper

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate step in comparative genomics analysis that aligns three or more biological sequences of similar length. MSA is an NP-hard problem for which no efficient algorithm exists to perform this in a reasonable amount of time. However, humans across evolution have developed special intuition to identify visual patterns in short periods of time. Hence, a citizen science approach can be devised to solve the MSA problem by transforming it into a human computing game on creating visually similar patterns. In this paper, we introduce the mobile game "Genenigma", which harnesses the human computing capability to align multiple sequences of genomes and use the results to help geneticists to understand the genetic code. The usability and performance scores of "Genenigma" predicts a larger user base than existing mobile games built for this purpose.

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2019
Conference paper

Abstract

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https://infoscience.epfl.ch/record/268297?ln=en

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Multiple sequence alignment

Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.

Comparative genomics

Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms.

Sequence alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.

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