Minimal Absent Words in Prokaryotic and Eukaryotic Genomes

Abstract

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates.

Lost Strings in Genomes: What Sense Do They Make?

“…This idea, in few various forms, has been formulated earlier [11,12]. Related ideas on the impact of the avoided strings on the structure (and functioning) of cancer genes is discussed in [8]; a comparative study of the avoided stings observed in assembling of a human genome is provided by [7], meanwhile, this study seems to be rather speculative.…”

Parallelising the Computation of Minimal Absent Words

“…The most comprehensive study on the significance of absent words is probably [2]; in this, the authors suggest that the deficit of certain subsets of absent words in vertebrates may be explained by the hypermutability of the genome. It was later found in [9] that the compositional biases observed in vertebrates in [2] are not uniform throughout different sets of minimal absent words. Moreover, the analyses in [9] support the hypothesis that minimal absent words are inherited through a common ancestor, in addition to lineage-specific inheritance, only in vertebrates.…”

“…It was later found in [9] that the compositional biases observed in vertebrates in [2] are not uniform throughout different sets of minimal absent words. Moreover, the analyses in [9] support the hypothesis that minimal absent words are inherited through a common ancestor, in addition to lineage-specific inheritance, only in vertebrates. In [8], the minimal absent words in four human genomes were computed, and it was shown that, as expected, intra-species variations in minimal absent words were lower than inter-species variations.…”

“…An implementation of this algorithm is currently, and to the best of our knowledge, the fastest available for the computation of minimal absent words. With the continuous efforts in whole-genome sequencing, the computation of minimal absent words remains the main bottleneck in analysing a large set of large genomes [8,9,17]. Hence due to the large amounts of data being produced, it is desirable to further engineer this computation.…”

Extraction of Infrequent Simple Motifs from a Finite Set of Sequences using a Lattice Structure

“…For example, searching rare motifs is an important task to identify absent words in genomic sequences [9,10,20]. Moreover, to identify proteins involved in parasitism, it is important to search the infrequent motifs [19].…”