Linear time minimum segmentation enables scalable founder reconstruction
Background We study a preprocessing routine relevant in pan-genomic analyses: consider
a set of aligned haplotype sequences of complete human chromosomes. Due to the …
a set of aligned haplotype sequences of complete human chromosomes. Due to the …
[HTML][HTML] Applying the positional Burrows–Wheeler transform to all-pairs hamming distance
Crochemore et al. gave in WABI 2017 an algorithm that from a set of input strings finds all
pairs of strings that have Hamming distance at most a given threshold. The proposed …
pairs of strings that have Hamming distance at most a given threshold. The proposed …
Linear time maximum segmentation problems in column stream model
We study a lossy compression scheme linked to the biological problem of founder
reconstruction: The goal in founder reconstruction is to replace a set of strings with a smaller …
reconstruction: The goal in founder reconstruction is to replace a set of strings with a smaller …
Identifying maximal perfect haplotype blocks
The concept of maximal perfect haplotype blocks is introduced as a simple pattern allowing
to identify genomic regions that show signatures of natural selection. The model is formally …
to identify genomic regions that show signatures of natural selection. The model is formally …
Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster
Q Wang, RA Elworth, TR Liu… - … Workshop on Algorithms …, 2019 - drops.dagstuhl.de
As sequence databases grow, characterizing diversity across extremely large collections of
genomes requires the development of efficient methods that avoid costly all-vs-all …
genomes requires the development of efficient methods that avoid costly all-vs-all …
Constructing founder sets under allelic and non-allelic homologous recombination
Homologous recombination between the maternal and paternal copies of a chromosome is
a key mechanism for human inheritance and shapes population genetic properties of our …
a key mechanism for human inheritance and shapes population genetic properties of our …
Linear Time Maximum Segmentation
D Kosolobov, V Mäkinen¹ - … 2019, Segovia, Spain, October 7–9 …, 2019 - books.google.com
We study a lossy compression scheme linked to the biological problem of founder
reconstruction: The goal in founder reconstruction is to replace a set of strings with a smaller …
reconstruction: The goal in founder reconstruction is to replace a set of strings with a smaller …