منابع مشابه
Parallelising the Computation of Minimal Absent Words
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their computation also provides a fast alternative for measuring approximation in sequence comparison. There exists an O(n)-time and O(n)-space algorithm for computin...
متن کاملLinear-Time Sequence Comparison Using Minimal Absent Words & Applications
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, ca...
متن کاملMinimal Absent Words in Four Human Genome Assemblies
Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, ...
متن کاملMinimal Absent Words in Prokaryotic and Eukaryotic Genomes
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 i...
متن کاملMinimal absent words in a sliding window & applications to on-line pattern matching
An absent (or forbidden) word of a word y is a word that does not occur in y. It is then called minimal if all its proper factors occur in y. There exist linear-time and linear-space algorithms for computing all minimal absent words of y (Crochemore et al., 1998, Belazzougui et al., 2013, Barton et al., 2014). Minimal absent words are used for data compression (Crochemore et al., 2000, Ota and ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2009
ISSN: 1471-2105
DOI: 10.1186/1471-2105-10-137