Related papers: Zimin patterns in genomes
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…
We investigate the number of inverted repeats observed in 37 complete genomes of bacteria. The number of inverted repeats observed is much higher than expected using Markovian models of DNA sequences in most of the eubacteria. By using the…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
In bioinformatics, minimizers have become an inescapable method for handling $k$-mers (words of fixed size $k$) extracted from DNA or RNA sequencing, whether for sampling, storage, querying or partitioning. According to some fixed order on…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
A word $x$ that is absent from a word $y$ is called minimal if all its proper factors occur in $y$. Given a collection of $k$ words $y_1,y_2,\ldots,y_k$ over an alphabet $\Sigma$, we are asked to compute the set…
A permutation $\sigma\in\mathfrak{S}_n$ is simsun if for all $k$, the subword of $\sigma$ restricted to $\{1,...,k\}$ does not have three consecutive decreasing elements. The permutation $\sigma$ is double simsun if both $\sigma$ and…
In this thesis, we consider the problem of characterizing and enumerating sets of polyominoes described in terms of some constraints, defined either by convexity or by pattern containment. We are interested in a well known subclass of…
This paper investigates pattern avoidance in linear extensions of a certain class of partially ordered set. Since the question of enumerating pattern avoiding linear extensions of posets in general is a very hard one, we focus instead on…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
We say that a word $w$ on a totally ordered alphabet avoids the word $v$ if there are no subsequences in $w$ order-equivalent to $v$. In this paper we suggest a new approach to the enumeration of words on at most $k$ letters avoiding a…
Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
There is a deep connection between permutations and trees. Certain sub-structures of permutations, called sub-permutations, bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study enumerative and…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome…