Related papers: An Assessment of PC-mer's Performance in Alignment…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…
Enormous volumes of short reads data from next-generation sequencing (NGS) technologies have posed new challenges to the area of genomic sequence comparison. The multiple sequence alignment approach is hardly applicable to NGS data due to…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are…
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
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…
Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…