More @ http://news.yale.edu/2013/10/17/researchers-rewrite-entire-genome-and-add-healthy-twist

News Reference: Yale news

Image Source: Sciencedaily.

Job Description: We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of paris.

Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.

Title: A novel integrative platform for large scale protein annotation that exploits a multitude of diversified probabilistic models in several protein signature databases.

We propose a novel integrated approach for large scale protein annotation that will exploit an unprecedented amount of genomic data as well as sophisticated machine learning techniques and combinatorial optimization approaches taking advantages of High Performance Computing (HPC) environments. The idea is to uncover as much as possible the evolutionary processes of protein sequences that took place throughout the whole tree of life and that affected the evolution of a protein family. We have already demonstrated in a previous work that the problem of functional annotation is inherent to the ability of uncovering such paths. Now, we shall extend this approach to large scale genome annotation by considering 11 different protein databases, constituted by about 10^9 protein sequences, and by producing a large pool of diversified probabilistic models coding for about 10^7 evolutionary protein pathways. Such models will be used to search for specific domains in genomes to be annotated. Our previous methodology needs to be fundamentally improved to deal with this large amount of biological data. In this project, we shall work on the algorithms to reduce the space of models and the search complexity, and we shall implement some important algorithmic changes towards the realization of a powerful integrated annotation tool.

Where: This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.

Start date: September 1st, 2014
Contact Person: Alessandra Carbone
Contact: alessandra.carbone@lip6.fr

• January 20th, 2016 - New! Bpipe 0.9.9 released!
• Download latest, all
• Documentation
• Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

Address of the bookmark: https://github.com/al2na/methylKit

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

• BLAST Tool: added support for local custom BLAST databases
• Graphical Sequence View: added log scaling option for graph tracks
• Generic Table View: new tutorial added

Bug Fixes and Improvements

• Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
• Tree View: layout updated to better accommodate nodes of different sizes
• Table Import Dialog (MacOS): fixed issue with table visibility
• Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
• Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
• Graphical Sequence View: fixed protein coloration methods
• Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
• Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
• Search View: ORF Finder – fixed incorrect protein lengths
• Fixed bug with not opening project file (.gbp) on a click
• Fixed issues in GVF import
• Fixed BLAST Search tool against NCBI databases not working
• Fixed tblastn (protein BLAST) not working in standalone mode
• Fixed GTF export failure

More at http://mrfast.sourceforge.net/manual.html

Address of the bookmark: http://mrfast.sourceforge.net/manual.html

Address of the bookmark: https://github.com/dentearl/mafTools

C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3