BOL: Related items

Genetics, epigenetics and disease

Fri, 27 Sep 2013 11:32:55 -0500

Royal Society GlaxoSmithKline Prize Lecture given by Professor Adrian Bird CBE FMedSci FRS on Tuesday 22 January 2013. Adrian Bird CBE FMedSci FRS is the Buchanan Chair of Genetics at the University of Edinburgh. The human genome sequence has been available for more than a decade, but its significance is still not fully understood. While most human genes have been identified, there is much to learn about the DNA signals that control them. This lecture described an unusually short DNA sequence, just two base pairs long, CG, which occurs in several chemically different forms. Defects in signalling by CG are implicated in disease. For example, the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the activity of genes. The Royal Society GlaxoSmithKline Prize Lecture is awarded for original contributions to medical and veterinary sciences published within ten years from the date of the award.

Update Genome Workbench 2.7.15 released

Surabhi Chaudhary — Wed, 26 Feb 2014 16:12:17 -0600

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

New Features in Genome Workbench 2.7.15

Multiple Alignment View: implemented adaptive feature display when zooming in
Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
Multiple Pane View: fixed crash on loading BLAST results
Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
Text View / Flat File: fixed Mac OS rendering issues
Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
File Import: optimization improvement to speed up load of files containing multiple project items
File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
Mac OS: improved tooltips for toolbar buttons
Phylogenetic Tree Builder Tool: improved diagnostics of errors
Multiple Alignment View: optimizations to avoid main GUI freezes
Open Dialog: removed duplicate elements in table of genomes (load Genome)
PDF export: fixed issue with XREF table errors
Tree View: fixed issues with showing Force Layout progress on Mac OS
Tree View: PDF export fixed issues for showing labels of collapsed nodes
Tree View: added an option to stop layout
Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

Nuclear Dynamics Lab

Thu, 17 Jul 2014 15:03:27 -0500

Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.

More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/

Rosalind Bioinformatics problems !!!

Abhi — Thu, 18 Dec 2014 10:32:48 -0600

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

seqloc 0.6

Gudiya Pal — Sun, 28 Dec 2014 12:51:29 -0600

The Bio.SeqLoc modules in seqloc are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in eukaryotic genomes.

Handle sequence locations for bioinformatics http://www.ingolia-lab.org/seqloc-tutorial.html

Address of the bookmark: http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6

Postdoctoral Fellowship in Bioinformatics at pesolelab

Thu, 01 Oct 2015 07:20:48 -0500

Job Description: Bioinformatics postdoc positions are available in the area of genomics with main focus on exome and RNAseq technologies by ultra high-throughput sequencing platforms. Successful applicants should have the following qualities:

1) demonstrated experience in Bioinformatics research,
2) programing experience (python and/or R, C and C++ are very welcome),
3) knowledge of Linux/Unix environment,
4) experience in handling deep-seq data,
5) highly motivated and hard working, and
6) interested to work with a multi-disciplinary team combining bioinformatics, genomics, computational biology approaches with experimental biology.

Our research interest covers different areas of bioinformatics and genomics in order to achieve a deeper understanding of gene and genome structure and function (please look at our PubMed publications for more details about our research http://www.ncbi.nlm.nih.gov/pubmed/?term=pesole+g).

Interested applicants should email the curriculum vitae to Prof. Graziano Pesole at graziano.pesole@uniba.it or Dr. Ernesto Picardi at Ernesto.picardi@uniba.it.

Start date: immediate

Duration: up to 24 months
Contact Person (Referent): Ernesto Picardi
Ref. E-Mail: ernesto.picardi@uniba.it
Tel: +390805443308
Fax: +390805443317

Group Web Page: http://www.pesolelab.it/

Alignment of closely related whole genomes/scaffolds

Rahul Nayak — Fri, 29 Jan 2016 10:37:27 -0600

With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments.

Please report new whole genome alignment tools under comment sections.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

UCSC Genome Browser and Blat software !

Jit — Thu, 18 Feb 2016 03:18:57 -0600

This directory contains Genome Browser and Blat application binaries built for standalone
command-line use on various supported Linux and UNIX platforms. To determine which set of binaries
to download, type "uname -a" on the command line to display your machine type. In most cases the
usage statement for the application can be viewed by running the binary with no arguments.

The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. A
license is required for commercial download and installation of these binaries, with the exception
of items built from the following source code directories, which are freely available for all uses:

- kent/src/utils (includes big* tools)
- kent/src/lib
- kent/src/hg/autoSql
- kent/src/hg/autoXml

For information about commercial licensing of the Genome Browser software, see
http://genome.ucsc.edu/license/. The Blat and In-Silico PCR software may be commercially
licensed through Kent Informatics (http://www.kentinformatics.com).

More at http://hgdownload.cse.ucsc.edu/admin/exe/

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/

CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.

Jit — Tue, 26 Apr 2016 11:38:10 -0500

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Canu is a hierachical assembly pipeline which runs in four steps:

Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

Hagfish - assess an assembly through creative use of coverage plots

Abhi — Fri, 20 May 2016 19:08:17 -0500

Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment.

Hagfish requires a reference sequence and a paired end re-sequencing data set. Hagfish has more power the larger the insert size of the paired end library is.

Quick links: Installation,Operation, Read mappers, Hagfish scripts, Hagfish plots

Address of the bookmark: https://github.com/mfiers/hagfish