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July 12, 2011: Public presentation of Polloc and Polloc-* tools
The Polloc library and derived tools (Polloc-V and Polloc-C) were presented in the public defense of internship period of Luis M. Rodriguez-R at the UM2 as last requirement for the Master IC - Bioinformatics. The slides are available in .mov and .pdf formats.
March 26, 2011: The code behind the VNTRs analysis tool goes public
The generic package for Polymorphic Loci analysis (Polloc) that serves as basis to the VNTRs analysis tool, is now public.
March 23, 2011: Advance report for the VNTRs analysis tool
Complex and large analysis (such as analysis, grouping and extension of VNTR loci in several genomes) take long times. There is no easy way to reduce these times (despite our efforts on algorithmic optimizations), but we can [at least] provide a short summary of the advance. Now, the screen keeps the user up to date on the advance of the analysis, displaying not only the elapsed time, but also the number of detected repetitive loci, analysed genomes, grouped VNTRs and extended groups.
March 22, 2011: Extend VNTRs, detect hard-to-find loci
The web interface of the VNTRs detection tool supports now the 'Extend Groups' option, that becomes active when 'Build Groups' is selected. When enabled, the extension task takes the groups, build multiple alignments per group (using up and downstream sequences) and searches those regions back in the genomes in order to detect VNTRs too small or too degenerated to be detected with a regular repeat search.
March 21, 2011: VNTRs big groups bug solved
A previous bug restricted VNTRs grouping to some seven or eight genomes. The bug (a.k.a. Issue BME #1) is now solved, and large jobs can be submitted (tested with up to ten genomes at once).
March 9, 2011: Laboratory accounts
Members from registered laboratories can now enjoy special privileges, such as additional genomes and up to three input files in the VNTRs detection tool. To sign in, use the link in the top-right corner.
March 2, 2011: VNTRs groping
The VNTRs detection tool now includes a new feature: Grouping. Now, you can automatically extract and compare the flanking regions of the VNTRs in order to build groups of loci, easing the development of diversity and typing tools for based on VNTRs.
March 1, 2011: Multi-genomes VNTRs detection
The VNTRs detection tool is now able to handle several genomes at a time.