PCI Math Comp Biol

188

Title

General encoding of canonical *k*-mersuse asterix (*) to get italics

Authors

Roland WittlerPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year

2023

Picture

Abstract

To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are encoded as integers, e.g., applying some bijective mapping between all possible σ^k k-mers and the interval [0,σ^k-1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0,σ^k-1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0,σ^k/2-1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.

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Keywords

canonical k-mers, k-mers, q-grams, encoding

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields

Combinatorics, Computational complexity, Genomics and Transcriptomics

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Pierre Peterlongo suggested: Maybe RIccardo Vicedomini could be intersted Riccardo Vicedomini <riccardo.vicedomini@irisa.fr> No need for them to be recommenders of PCI Math Comp Biol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

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Submission date

2023-03-13 17:01:37

Recommender

Paul Medvedev

Reviewers

Anonymous

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