Alignment-free sequence comparison: benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …
genome phylogeny to the classification of protein families, identification of horizontally …
De novo genome assembly and in natura epigenomics reveal salinity‐induced DNA methylation in the mangrove tree Bruguiera gymnorhiza
Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low
nutrition, and fluctuating salinity in coastal zones. However, little is known about the …
nutrition, and fluctuating salinity in coastal zones. However, little is known about the …
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
Motivation Word-based or 'alignment-free'algorithms are increasingly used for phylogeny
reconstruction and genome comparison, since they are much faster than traditional …
reconstruction and genome comparison, since they are much faster than traditional …
Alignment-free method for DNA sequence clustering using Fuzzy integral similarity
A larger amount of sequence data in private and public databases produced by next-
generation sequencing put new challenges due to limitation associated with the alignment …
generation sequencing put new challenges due to limitation associated with the alignment …
A greedy alignment-free distance estimator for phylogenetic inference
Background Alignment-free sequence comparison approaches have been garnering
increasing interest in various data-and compute-intensive applications such as phylogenetic …
increasing interest in various data-and compute-intensive applications such as phylogenetic …
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Map** and Alignment-Free Sequence Comparison
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these
approaches can be improved if binary patterns representing match and don't-care positions …
approaches can be improved if binary patterns representing match and don't-care positions …
Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences
Word-based or 'alignment-free'sequence comparison has become an active research area
in bioinformatics. While previous word-frequency approaches calculated rough measures of …
in bioinformatics. While previous word-frequency approaches calculated rough measures of …
Longest common factor after one edit operation
It is well known that the longest common factor (LCF) of two strings over an integer alphabet
can be computed in time linear in the total length of the two strings. Our aim here is to …
can be computed in time linear in the total length of the two strings. Our aim here is to …
Algorithmic framework for approximate matching under bounded edits with applications to sequence analysis
We present a novel algorithmic framework for solving approximate sequence matching
problems that permit a bounded total number k of mismatches, insertions, and deletions. The …
problems that permit a bounded total number k of mismatches, insertions, and deletions. The …
Linear-Time Algorithm for Long LCF with Mismatches
In the Longest Common Factor with $ k $ Mismatches (LCF $ _k $) problem, we are given
two strings $ X $ and $ Y $ of total length $ n $, and we are asked to find a pair of maximal …
two strings $ X $ and $ Y $ of total length $ n $, and we are asked to find a pair of maximal …