BOL: Related items

BIOINFORMATICS

Wed, 28 Aug 2013 19:16:33 -0500

This is a promo video for the brand new cross-boarder branch of study - BIOINFORMATICS. It´s a co-operation between Johannes Kepler University in Linz (Austria) and University of South Bohemia in České Budějovice (Czech Republic). Written, Edited and Directed by, DOP, VFX: Jan Míka Sound by: Mirek Šmilauer Narrator: Jack Bright Produced by: FILMOFON (http://www.filmofon.cz) Released: Nov 2012

TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Poonam Mahapatra — Tue, 15 May 2018 09:52:28 -0500

TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a desktop computer, therefore allowing researchers to locally analyze their metagenomic sequence data or integrate it into their pipelines.

Address of the bookmark: http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa

R and Bioconductor Tutorial

Jitendra Narayan — Fri, 23 Aug 2013 08:23:59 -0500

This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that biologists need to perform some basic analysis: load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).

You can add more tutorial links in comments if found new pages.

Address of the bookmark: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

What is Bioinformatics?

Wed, 28 Aug 2013 06:53:05 -0500

Illustration and Animation: Rachel Robinson Script: Tiffany Trent Voice-over: Kris Monger Sound: Glisten Carefully by Guennadi Malyshevski

Opera: An optimal genome scaffolding program

Jit — Mon, 27 Nov 2017 10:18:20 -0600

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes.

Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.

Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

Address of the bookmark: https://sourceforge.net/projects/operasf/

IBM Research Computational Biology Center

Thu, 29 Aug 2013 08:43:59 -0500

The IBM Computational Biology Center embraces activities at Yorktown Heights, with strong affiliations with activities at Almaden and other IBM Research Centers. Computational Biology (CompBio) including bioinformatics is the study of how computer systems can manage, analyze, and simulate the complex structures and processes inherent in living systems. CompBio Research at IBM spans pattern recognition in sequences, structures and processes, the studying of systems ranging from single protein molecules through to complex molecular interactions, and the data analysis, interpretation and reverse-engineering of complex disease-lifestyle-genomic interactions for fuller biological understanding. "CompBio" has a flavor of its own independant of its parents, biology and computer science. Nonetheless, CompBio is inherently a multi- disciplinary field with important applications in biology, chemical physics, materials science, agriculture, chemistry and ultimately nanotechnology.

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

May 17, 2013 - Differential Network Analysis

Wed, 04 Sep 2013 16:22:28 -0500

Steve Horvath presents Differential Network Analysis at the UCLA Human Genetics/Biostatistics Network Course

Mash: fast genome and metagenome distance estimation using MinHash

Jit — Tue, 12 Dec 2017 17:30:12 -0600

Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10.7.

See http://mash.readthedocs.org for more information.

Address of the bookmark: https://github.com/marbl/Mash/releases