Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

February 13, 2021
Open Access

S-conLSH: alignment-free gapped mapping of noisy long reads.

BMC Bioinformatics
Angana ChakrabortySanghamitra Bandyopadhyay
January 21, 2021
Preprint
Open Access

SAINT: automatic taxonomy embedding and categorization by Siamese triplet network

BioRxiv : the Preprint Server for Biology
Y. Y. LuYing Wang
January 12, 2021

Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers.

Forensic Science International. Genetics
August E WoernerBruce Budowle
January 8, 2021
Open Access

Efficient association mapping from k-mers-An application in finding sex-specific sequences.

PloS One
Zakaria MehrabAtif Rahman
December 29, 2020
Open Access

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments.

Genome Research
Ales VarabyouMihaela Pertea
December 21, 2020
Preprint
Open Access

RedOak: a reference-free and alignment-freestructure for indexing a collection of similargenomes

BioRxiv : the Preprint Server for Biology
C. AGRETAlban Mancheron
December 20, 2020
Open Access

Male Linked Genomic Region Determines Sex in Dioecious Amaranthus palmeri.

The Journal of Heredity
Cátia José NevesMarkus G Stetter
December 18, 2020
Open Access

Alignment free identification of clones in B cell receptor repertoires

Nucleic Acids Research
Ofir LindenbaumSteven H Kleinstein
December 9, 2020
Open Access

Information Theory in Computational Biology: Where We Stand Today

Entropy
Pritam ChandaRasna Walia
December 9, 2020
Open Access

Sequence Comparison Without Alignment: The SpaM Approaches

Methods in Molecular Biology
Burkhard Morgenstern
December 4, 2020
Preprint
Open Access

Aperture: Accurate detection of structural variations and viral integrations in circulating tumor DNA using an alignment-free algorithm

BioRxiv : the Preprint Server for Biology
H. LiuXiaoyue Wang
November 26, 2020
Comment / Editorial
Open Access

Feature frequency profile-based phylogenies are inaccurate.

Proceedings of the National Academy of Sciences of the United States of America
Yuanning LiAntonis Rokas
November 26, 2020

New Genome Sequence Detection via Natural Vector Convex Hull Method

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Ruzhang ZhaoStephen S-T Yau
November 16, 2020
Preprint
Open Access

Fast Alignment-Free Similarity Estimation By Tensor Sketching

BioRxiv : the Preprint Server for Biology
A. JoudakiGunnar Ratsch
October 19, 2020
Preprint
Open Access

Phylogenetic placement of short reads without sequence alignment

BioRxiv : the Preprint Server for Biology
M. Blanke, Burkhard Morgenstern
October 13, 2020
Open Access

Seeker: alignment-free identification of bacteriophage genomes by deep learning

Nucleic Acids Research
Noam AuslanderEugene V Koonin
October 3, 2020
Preprint
Open Access

A novel algorithm to accurately classify metagenomic sequences

BioRxiv : the Preprint Server for Biology
S. SahaSanguthevar Rajasekaran
October 1, 2020
Preprint
Open Access

I-CONVEX: Fast and Accurate de Novo Transcriptome Recovery from Long Reads

BioRxiv : the Preprint Server for Biology
Sina BaharloueiD. Tse

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