WAMI: a web server for the analysis of minisatellite maps

Abstract

BackgroundMinisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time.ResultsIn this paper we present WAMI, a web-server for the analysis of minisatellite maps. It performs the above mentioned computational tasks using efficient algorithms that take the model of map evolution into account. The WAMI interface is easy to use and the results of each analysis task are visualized.ConclusionsTo the best of our knowledge, WAMI is the first server providing all these computational facilities to the minisatellite community. The WAMI web-interface and the source code of the underlying programs are available at http://www.nubios.nileu.edu.eg/tools/wami.

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically

“…To compare the sequences of coded repeats DisTAL uses the program ARLEM (also referred to as WAMI) (Abouelhoda et al, 2010 ) which was designed to compare minisatellite maps. A minisatellite map is a sequence of symbols that represents tandem arrays of short repetitive DNA segments such that the set of symbols is in one-to-one correspondence with the set of distinct repeats (Abouelhoda et al, 2010 ).…”

“…DisTAL additionally uses the module Algorithm::NeedlemanWunsch ( http://search.cpan.org/~vbar/Algorithm-NeedlemanWunsch-0.03/lib/Algorithm/NeedlemanWunsch.pm ) to align repeats and the C++ program ARLEM version 1.0 (Abouelhoda et al, 2010 ) to align sequences of coded repeats. Penalty parameters values for NeedlemanWunsch alignments are gap: 0, mismatch: −1, match: +1, alignment scores are normalized by dividing the score by the maximum length among the analyzed sequences and multiplying by 100 so they can be used by ARLEM.…”

“…In this paper we describe two methods, DisTAL and FuncTAL, to align and classify TAL effector gene sequences according to their central repeat region. With DisTAL, we propose a tool that infers phylogenetic relationships between genes by considering each repeat as a unit and calculating distances between arrays of repeats, using an algorithm initially designed to compare microsatellite sequences (ARLEM version 1.0, Abouelhoda et al, 2010 ). FuncTAL aims to find functionally-related TAL effectors by calculating similarities in binding probabilities according to the RVD-DNA code.…”

Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

“…With the recent development of next-generation sequencing technologies, an ever-increasing number of plant species have been studied and vast amounts of sequence data accumulated. Next-generation sequencing provides a convenient way to search for the presence of mini-satellite repeated sequences [14,15]. As a major class of repetitive DNA, mini-satellites consist of tandemly organized monomers.…”

“…A remarkable advance in the knowledge of repetitive sequences has occurred in recent years because of the introduction of next-generation sequencing technologies [12]. Bioinformatic pipelines or web servers have provided computational facilities for the identification of mini-satellites for next-generation sequence data [13][14][15]. The availability of genome sequences allows…”