BOL: Related items

The Story of You: ENCODE and the human genome

Sat, 24 Aug 2013 18:49:03 -0500

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

Oldest Hominin DNA Sequenced

Surajeet — Fri, 27 Dec 2013 19:58:31 -0600

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, about 700,000 years ago. "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features," says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm

Genome + Epigenome = New Understanding of the Pathogens in Your Food

Fri, 27 Sep 2013 11:30:45 -0500

UC Davis's Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology. www.pacb.com/microbe

List of bioinformatics open source projects/software.

Rahul Nayak — Tue, 21 Jan 2014 14:28:37 -0600

Open source software is software that can be freely used, changed, and shared (in modified or unmodified form) by anyone. Open source software is made by many people, and distributed under licenses that comply with the Open Source Definition.The Open Source Initiative (OSI) is a global non-profit that supports and promotes the open source movement. Followings are the OS bioinformatics projects/software :

.NET Bio

http://blogs.msdn.com/b/msr_er/archive/2011/10/18/microsoft-biology-foundation-evolves-into-new-toolkit-net-bio.aspx

A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.

AMPHORA ("AutoMated Phylogenomic infeRence Application")

http://wolbachia.biology.virginia.edu/WuLab/Software.html

Metagenomics analysis software

Anduril

http://www.anduril.org/anduril/site/

Component-based workflow framework for data analysis

Armadillo workflow platform

Tool for designing and executing phylogenetic workflows

AutoDock

http://autodock.scripps.edu/

suite of automated docking tools

Biochemical Algorithms Library (BALL)

http://www.ball-project.org/

C++ library and framework for molecular modeling and visualization designed for rapid prototyping

Bio4j

http://bio4j.com/

Bio4j is a bioinformatics platform and graph based database built around most data available in UniProt KB(Swiss-Prot + TrEMBL), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB

Bioclipse

www.bioclipse.net

Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

Bioconductor

http://www.bioconductor.org/

R (programming language) language toolkit

Bioinformatics Learning Tutorial (BLT)

http://sourceforge.net/projects/biotutorial/

Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation

BioHaskell

http://biohaskell.org/

Haskell (programming language)

BioJava

http://biojava.org/wiki/Main_Page

Java (programming language)

BioMOBY

http://biomoby.org/

registry of web services

BioPerl

http://www.bioperl.org/wiki/Main_Page

Perl language toolkit

BioPHP

http://www.biophp.org/

PHP language toolkit

Biopython

http://biopython.org/wiki/Main_Page

Python language toolkit

BioRails

https://github.com/biorails

a data management system designed to support researchers in drug discovery

BioRuby

http://bioruby.org/

Ruby language toolkit

BioSmalltalk

https://code.google.com/p/biosmalltalk/

Smalltalk language toolkit

BioUno

http://www.biouno.org/

BioUno is a project that applies Continuous Integration tools and techniques in Bioinformatics. It uses Jenkins and its plug-in API to create biology workflows and manage computer clusters.

caCORE

ontologic representation environment

caArray

https://cabig-stage.nci.nih.gov/community/tools/caArray

ontologic representation environment

EMBOSS

http://emboss.sourceforge.net/

Suite of packages for sequencing, searching, etc.

Gaggle

https://www.gaggle.net/

A framework for interoperability between systems biology software

Galaxy

http://galaxyproject.org/

Scientific workflow and data integration system

GenePattern

http://www.broadinstitute.org/cancer/software/genepattern/

Scientific workflow system that provides access to more than 150 genomic analysis tools

GeWorkbench

http://wiki.c2b2.columbia.edu/workbench/index.php/Home

Genomic data integration platform

GMOD

http://www.gmod.org/wiki/Main_Page

Toolkit for addressing many common challenges at biological databases.

GeneProf

http://www.geneprof.org/GeneProf/

A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq.

GeneTalk

http://www.gene-talk.de/

Tool for filtering sequence variants in VCF files. Network for scientists and clinicians for expertise and knowledge exchange. Database of annotations aboute sequence variants with clinically relevant information.

GenGIS

http://kiwi.cs.dal.ca/GenGIS/Main_Page

Application that allows users to combine digital map data with information about biological sequences collected from the environment.

GenomeSpace

http://www.genomespace.org/

Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools

GENtle

http://directory.fsf.org/wiki/GENtle

An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files

Integrated Genome Browser

http://bioviz.org/igb/

Java-based desktop genome browser

Integrative Genomics Viewer (IGV)

http://www.broadinstitute.org/igv/

High-performance desktop tool for interactive visual exploration of diverse genomic data

IntAct

http://www.ebi.ac.uk/intact/

molecular interaction database

InterMine

http://intermine.github.io/intermine.org/

Extensive data warehouse system for the analysis and integration of biological datasets

Java Treeview

http://jtreeview.sourceforge.net/

microarray data viewer

LabKey Server

http://labkey.com/

platform for integrating, analyzing and sharing data

OpenClinica

https://www.openclinica.com/

software for capturing and managing data in clinical trials

PromKappa

http://xbioinformatics.wordpress.com/tag/promkappa/

PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis.

MeV: Multi-Experiment Viewer

http://www.tm4.org/mev.html

a desktop application for the analysis, visualization and data-mining of large-scale genomic data

PathVisio

http://www.pathvisio.org/

a desktop software for drawing, analysis and visualization of biological pathways

REDCRAFT

software for determining tertiary protein structure given assigned Residual Dipolar Coupling data

SAM Tools

Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments

Staden Package

Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin.

STAMP

Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results.

supraHex

An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map

Taverna workbench

Tool for designing and executing workflows

TGAC Browser

Genome Browser, visualisation solutions for big data in the genomic era

T-REX WebServer

Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models)

UGENE

integrated bioinformatics tools

Visomics

bioinformatics tools for omics data

Genome Analysis Toolkit 1.0 (GATK 1.0)

a software package to analyse next-generation resequencing data

Genetic code - Amino Acid

Poonam Mahapatra — Sun, 26 Oct 2014 07:45:58 -0500

The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

The image summarise all in one.

More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

The 2014 CeMM PhD Program

Wed, 05 Feb 2014 06:03:15 -0600

For our next PhD Program starting in October 2014 we are looking for exceptionally motivated PhD candidates with a keen interest in genomics and medicine and a strong interest to work in teams.

The 2014 CeMM PhD Program will focus on two thematic areas: INFECTION and CANCER, that are built on the pillars of epigenetics, bioinformatics and systems biology, chemical biology and the mechanism of action of drugs, high-throughput genetics, genomics and proteomics, and molecular and cell biology.

The choice of this strategic focus rests on the synergies between immunology, infection and cancer in pathophysiological and technological terms. It furthermore reflects the strength of the current CeMM faculty, itself built around the historical and contemporary expertise in immunology and cancer of the Medical University of Vienna.

As a CeMM PhD student you will get the chance to work at the cutting edge of interdisciplinary molecular medicine research and be trained by the entire CeMM and associated faculty to become one of the scientists shaping the future of molecular medicine.
Requirements

To be eligible to enroll in the CeMM PhD Program all candidates are required to have a bachelor’s or master’s degree in medicine, biology, chemistry, bioinformatics, mathematics or any scientific/technical, subject-relevant degree. Candidates do not need to have completed their degree at the time of application, however they must have obtained their final degree certificate by mid-September. The working language at CeMM is English, so excellent written and oral communication skills in English are required.
Timeline

Applications open on 20th January and close on 20th March 2014.
Two references are required to be submitted through the online system by 31st March 2014.
All complete candidate applications are reviewed by the CeMM Faculty in early April.
Selected candidates are invited to a Skype panel interview in late April.
Shortlisted candidates are then invited to Vienna in May for a full interview process, including an opportunity to introduce yourself through a presentation and interview rounds, meet research group members, and attend an informal dinner to get to know the Faculty members and learn more about their research.
Positions are offered by CeMM Faculty in June.
Start of PhD Program: 1st October 2014 .

Contact

Binia Maria Günther, BEd BA
Human Resources Manager
bguenther@cemm.oeaw.ac.at

Catherine Lloyd, Ph.D.
PhD and Postdoc Program Manager
clloyd@cemm.oeaw.ac.at

More Info: www.cemm.oeaw.ac.at/phd-program/application/

Genome Annotation Transfer Utility (GATU)

Jit — Mon, 29 May 2017 05:54:53 -0500

Genome Annotation Transfer Utility (GATU) was designed to facilitate quick, efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strain of SARS coronavirus is sequenced, it is possible, using GATU, to automatically annotate the new strain using a previously-annotated strain of SARS CoV. This saves researchers from tedious manual annotation of these sequences.

The program utilizes tBLASTn and BLASTn algorithms to map genes from the reference genome (the annotated strain) to the new sequence (the unannotated strain). The goal is to annotate the majority of the new genome’s genes in a single step. ORFs present in the target genome and absent from the reference genome are also identified; these ORFs can be further analyzed using BLAST, VGO and BBB. Afterwards, they can either be accepted for/rejected from annotation. GATU can handle multiple-exon genes as well as mature peptides. Although it was designed for use with viral genomes, GATU can also be used to help annotate larger genomes (ie. bacterial genomes).

The output is saved in GenBank, XML, or EMBL file format.

Address of the bookmark: https://virology.uvic.ca/help/tool-help/help-books/genome-annotation-transfer-utility-gatu-documentation/

JRF @ MANIT

Sun, 02 Feb 2014 03:07:58 -0600

MAULANA AZAD NATIONAL INSTITUTE OF TECHNOLOGY BHOPAL

No. CSE/14/1038

Walk in Interview for the post of JRF under TEQIP-II

SN Department – Qualification Post Graduation – Time

1 Bio-Informatics & Mathematics M.Tech Bio-informatics/M.Sc.* Maths 10.00 AM

2 Biological Sciences M.Sc.* in any branch of Biological Sciences 10.30 AM

3 Chemical Engineering M.Tech Chemical Engineering 11.00 AM

4 Chemistry M.Sc.* Chemistry 11.30 AM

5 Civil Engineering M.Tech Structure/GeoTech. /Water -Resources/Hydraulics/Environment/Transport 12.00 Noon

6 GIS M.Tech GIS/Civil 12.30 PM

7 Computer Science & Engineering M.Tech CSE/Information Security 01.00 PM

8 Electrical Engineering M.Tech Electrical Derives 01.30 PM

9 Electronics & Communication M.Tech Digital Communication 02.00 PM

10 MSME M.Tech Material Science/ Mechanical/Metallurgy 02.30 PM

11 Physics M.Sc.* Physics 03.00 PM

* M.Sc. with NET/GATE qualified

Resume along with one passport size photograph and relevant documents are required at the time of interview

Amount of Fellowship: Rs 18000/-month+ HRA

Duration: 31st Dec 2014 (End of TEQIP-II project)

Date of Interview: 7th February 2014

Venue Institute Committee Room

http://www.manit.ac.in/manitbhopal/Year2014/Recruitment/Advertisement%20JRF.pdf

REGEN: Ancestral Genome Reconstruction for Bacteria

Rahul Nayak — Tue, 06 Mar 2018 05:02:36 -0600

REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order.

Address of the bookmark: http://www.mdpi.com/2073-4425/3/3/423

Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy

Tue, 11 Feb 2014 08:06:47 -0600

We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889