WAMI: a web server for the analysis of minisatellite maps

Abstract

Background: Minisatellites 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.

Results: In 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.

Conclusions: To 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.

Figure 1

A minisatellite map. Part (a): A minisatellite locus and the respective map. The locus contains five units classified into three distinct unit types denoted by the symbols a, b, and c. Part (b): The unequal cross over causes duplication of unit b leading to the map in Part (a) of this figure.

Figure 2

WAMI main web-interface. The upper sections include input of maps and cost file as well as some examples. A description of the example of the President Jefferson's dataset is shown. The lower section sets the option for building a phylogenetic tree over the input map. Note that there are other related tabbed pages, including introduction, web-service, download, and help/Blog pages. Right: The result page of WAMI. The output is organized into three categories: Alignment, phylogeny, and batch retrieval. In the alignment category, all pairwise alignments can be displayed. Here, an alignment between maps one and two (given in the left screen shot) is visualized. The replaced (match/mismatch) units are put above each other. An arc connecting two identical units corresponds to a duplication event, and an arc connecting two different units corresponds to a duplication followed by a mutation events. The sub-map composed of the units " bcaccbb" of the lower sequence emerged from the leftmost unit b of this sub-map. The duplication history was the one explained in the subsection about duplication history and alignment model. The category showing the phylogenetic tree appears only if this option was set. We provide the tree in text, JPEG (shown image), and PDF format. Finally, we provide a link to a compressed file containing all the input/output files of a WAMI run.

Figure 3

Phylogenetic trees. Left: Phylogenetic trees for a subset of the MS205 dataset, including individuals from different populations; Basque (BAS), UK, Surui (SU), Japanese (JAP), West African (Waf), and Zimbabweans (Z). (Here we use the original nomenclature distributed with the dataset.) Right: Phylogenetic tree for a subset of the MSY1 dataset including individuals from different populations. Individuals belonging to the same population are clustered together.

Figure 4

Structural variations histograms. (a): Histogram reported by WAMI for the MS205 dataset. The x-axis is the pivot-point normalized to the sequence lengths and the y-axis is its count. The red histogram is for the real dataset and the green histogram is for the randomized dataset. (See the original figures attached to the manuscript.) Accumulation at the right side indicates more variations at the 3' end. (b): Histogram for the subset of MS205 dataset including haplotype C. (c): Histogram of the MSY1 dataset, showing that the variations are bi-polar. (d): Histogram of MSY1, but after removing the units with Type 4 and 4a, showing that variations in this case accumulate only at the left side.

Figure 5

Duplication dynamics histograms. Left: Histogram to detect directional bias for the MSY1 dataset. The distribution of E_n of the randomized data is centered around zero. The peak at point 1 on the x-axis is for E_n of the original dataset, and it is clearly far from that of data with expected equal rates of left-to-right and right-to-left duplications. Right: Histogram to detect directional bias for the MS205 dataset. The peak on the left on the x-axis is for E_n of the original dataset.