Publications (12)
Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding
Bastien Cazaux, Eric Rivals
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data.…
Convergence of the number of period sets in strings
Eric Rivals, Michelle Sweering, Pengfei Wang
Consider words of length . The set of all periods of a word of length is a subset of . However, any subset of is not necessarily…
Accurate selfcorrection of errors in long reads using de Bruijn graphs
Leena Salmela, Riku Walve, Eric Rivals +1
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the…
Counting overlapping pairs of words
Eric Rivals, Pengfei Wang
A correlation is a binary vector that encodes all possible positions of overlaps of two words, where an overlap for an ordered pair of words (u,v) occurs if a suffix of word u matc…
Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model
Carole Chevalier, Jérôme Dorignac, Yahaya Ibrahim +9
Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) i…
The Compressed Overlap Index
Rodrigo Canovas, Bastien Cazaux, Eric Rivals
For analysing text algorithms, for computing superstrings, or for testing random number generators, one needs to compute all overlaps between any pairs of words in a given set. The…