Search · four archives
Search · four archives
13 papers · ranked by Valyu relevance
Yubo Sun, Gennian Ge
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length k is the insertion of the reversed and complemented copy of a substring of length k adjacent to its original position, while a palindromic duplication only inserts the reversed copy…
Ryosuke Yamano, Tetsuo Shibuya
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements (SCS-RC), naturally arises in bioinformatics applications, where for each input string…
Virginia Iannibelli, Isabella Caranzano, Giovanni Birolo, Cesare Rollo + 5 more
Codon usage bias is a central record of mutation, selection, drift, and translational constraints, but it is usually treated separately from generalized Chargaff symmetry, the tendency for words and their reverse complements to occur at similar frequencies in long DNA sequences. Here we ask whether codon usage contains…
Mohd Anwar, Mohd Arif Raza, Mohd Rashid, Muzibur Rahman Mozumder
In this paper, we study the structure of double cyclic codes of length $(γ,δ)$ over $\mathbb F_q+u\mathbb F_q, u^2=0$. We also study the dual of double cyclic code of length $(γ,δ)$ and give a minimal spanning set of double cyclic codes. Moreover, we study the necessary and sufficient conditions for a double cyclic…
Wu-Jun Li
We characterize perfect matchings on the Boolean hypercube {0, 1} n that are equivariant under the Klein four-group K 4 = ⟨comp,rev⟩ generated by bitwise complement and reversal. For n = 6, we prove there exists a unique K4-equivariant matching minimizing total Hamming cost among matchings using only comp or rev…
Shakir Ali, Amal S. Alali, Mohd Azeem, Atif Ahmad Khan + 2 more
Let e be a fixed positive integer and $n_{1},n_{2}$ be odd positive integers. The main objective of this article is to investigate the algebraic structure of double cyclic codes of length $(n_{1},n_{2})$ over the finite chain ring $(Re = F_{4e}+vF_{4e})$, where $v2=0$. Building upon this structural framework, we…
Richard Durbin
Skiplists (Pugh, 1990) are probabilistic data structures over ordered lists supporting 𝒪 (log N) insertion and search, which share many properties with balanced binary trees. Previously we introduced the graph Burrows-Wheeler transform (GBWT) to support efficient search over pangenome path sets, but current…
Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla + 4 more
Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this…
Authors not listed
A framework for catalysis based on categorical aperture selection rather than temporal acceleration is presented. Traditional catalysis theory describes catalysts as agents that accelerate reactions by lowering activation energies, implicitly treating time as the fundamental variable and reaction rate enhancement as…
Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla + 4 more
Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this…
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
Harry Stoltz, Thomas E. Kuhlman
Somatic genetic mosaicism arises when genomes diverge across cells during development, in part due to the activity of transposons (cut–paste) and retrotransposons (copy–paste). Standard sequence comparison methods are not motif-aware, penalizing mobile element insertions based on length rather than recognizing them as…
Acharya, Divya, Prasanna Poojary, Vadiraja Bhatta G. R
In this article, we study the algebraic structure of double cyclic codes of length (m, n) over F 4 and we give a necessary and sufficient condition for a double cyclic code over F 4 to be reversible. Also, we determine the algebraic structure of double cyclic codes of length (m, n) over F 4 + vF 4 with v 2 = v…