News ¶
- July 12, 2011: Public presentation of Polloc and Polloc-* tools
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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
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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
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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
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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
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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
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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
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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
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The VNTRs detection tool is now able to handle
several genomes at a time.