Search · four archives
Search · four archives
5 papers · ranked by Valyu relevance
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…
Roland Wittler
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 often 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…
Guillaume Marçais, C.S. Elder, Carl Kingsford
Sequences equivalent to their reverse complements (i.e., double-stranded DNA) have no analogue in text analysis and non-biological string algorithms. Despite this striking difference, algorithms designed for computational biology (e.g., sketching algorithms) are designed and tested in the same way as classical string…
Pelin Icer Baykal, Mike Simonov, Dhrithi Deshpande, Ful Belin Korukoglu + 8 more
Genomic research relies on accurate and reproducible computational analyses of DNA sequencing data to draw reliable biological conclusions. Read mapping, the process of aligning reads to a reference genome, is central to many applications, including variant detection and comparative genomics. While several tools have…
Ali Ghaffaari, Alexander Schönhuth, Tobias Marschall
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based…