Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

Abstract

In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free methods rely on exact word matches to estimate pairwise similarities or distances between the input sequences. By contrast, our new algorithms are based on inexact word matches. The first of these approaches uses the relative frequencies of so-called spaced words in the input sequences, i.e. words containing ‘don't care’ or ‘wildcard’ symbols at certain pre-defined positions. Various distance measures can then be defined on sequences based on their different spaced-word composition. Our second approach defines the distance between two sequences by estimating for each position in the first sequence the length of the longest substring at this position that also occurs in the second sequence with up to k mismatches. Both approaches take a set of deoxyribonucleic acid (DNA) or protein sequences as input and return a matrix of pairwise distance values that can be used as a starting point for clustering algorithms or distance-based phylogeny reconstruction. The two alignment-free programmes are accessible through a web interface at ‘Göttingen Bioinformatics Compute Server (GOBICS)’: http://spaced.gobics.de http://kmacs.gobics.de and the source codes can be downloaded.

Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer

“…For large-scale comparisons of genome-scale sequences, especially highly diverse ones, alignment-free methods of phylogeny construction have been increasingly used in the past few years23242526. There are two categories of alignment-free methods for phylogenomic analysis: one based on the statistics of word frequency, the other on Kolmogorov complexity and chaos theory27.…”

An Approach for TV Channel Recognition based on Audio

“…Although, The problem of time-shift can be solved based on FFT, frequency domain analysis can't solve the interrelationship on timing sequence accurately. Therefore, after steps of screening for j B , pairwise points should be checked in time domain so as to improve recognition accuracy based on high-level semantic [7]. In experiment, k is set to 3~8.…”

Enabling full‐length evolutionary profiles based deep convolutional neural network for predicting DNA‐binding proteins from sequence

“…Some sequence matches are also missed due to insertion and deletions between key residue positions of a novel protein. In such cases, direct methods of functional annotation, which rely on scanning a sequence through sliding windows or use global summary of sequence properties such as amino acid composition have proved useful . Protein‐function annotation on a large scale is done by use of Gene Ontologies .…”

“…In such cases, direct methods of functional annotation, which rely on scanning a sequence through sliding windows or use global summary of sequence properties such as amino acid composition have proved useful. [4][5][6][7][8] Protein-function annotation on a large scale is done by use of Gene Ontologies. 4 However, focusing on individual, well understood biological functions and annotating specific Biological functions gives much more power to a predictive method, as the annotations can incorporate knowledge specifically relevant for that system.…”