Anna Lindeberg,Guillaume E Scholz,Nicolas Wieseke et al.
Anna Lindeberg et al.
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying...
Anna Lindeberg,Guillaume E Scholz,Nicolas Wieseke et al.
Anna Lindeberg et al.
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying...
Bertrand Marchand,Nadia Tahiri,Shohreh Golpaigani Fard et al.
Bertrand Marchand et al.
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations con...
Exclusive functional signatures for gene annotation with vast OpenOrd layout [0.03%]
具有独特功能特征的基因注释以及使用Vast OpenOrd布局
Gleb Buzanov,Vsevolod Makeev
Gleb Buzanov
A biological study can produce a limited number of marker genes, not large enough to be used in gene set enrichment analysis. Here we suggest VOL-Gene, a graph-based algorithm that partitions all genes into non-overlapping classes of functi...
The path-label reconciliation (PLR) dissimilarity measure for gene trees [0.03%]
基因树的路径标签和解聚相似度测度(PER)
Alitzel López Sánchez,José Antonio Ramírez-Rafael,Alejandro Flores-Lamas et al.
Alitzel López Sánchez et al.
Background: In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approac...
b-move: faster lossless approximate pattern matching in a run-length compressed index [0.03%]
B-Move：在行程长度索引中进行更快的无损近似模式匹配
Lore Depuydt,Luca Renders,Simon Van de Vyver et al.
Lore Depuydt et al.
Background: Due to the increasing availability of high-quality genome sequences, pan-genomes are gradually replacing single consensus reference genomes in many bioinformatics pipelines to better capture genetic diversity....
Elizabeth S Allman,Hector Baños,John A Rhodes et al.
Elizabeth S Allman et al.
Inference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of the Tree of Blobs of a network, showing only the network's cut edges, can be perfor...
Jens Zentgraf,Sven Rahmann
Jens Zentgraf
Motivation: Short DNA sequences of length k that appear in a single location (e.g., at a single genomic position, in a single species from a larger set of species, etc.) are called unique k-mers. They are useful for placi...
Anchorage accurately assembles anchor-flanked synthetic long reads [0.03%]
精准组装带锚点的长reads拼接序列——Anchorrage算法
Xiaofei Carl Zang,Xiang Li,Kyle Metcalfe et al.
Xiaofei Carl Zang et al.
Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to acc...
Larissa L M Aguiar,Felipe A Louza
Larissa L M Aguiar
Finding shortest unique substrings (SUS) is a fundamental problem in string processing with applications in bioinformatics. In this paper, we present an algorithm for solving a variant of the SUS problem, the left-bounded shortest unique su...