BOL: Related items

Coronavirus Resources !

Neel — Wed, 25 Mar 2020 17:11:33 -0500

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

PHD SCHOLARSHIP DENMARK

Fri, 13 Jun 2014 13:44:07 -0500

ne PhD position is available at the Bioinformatics Center, Department of Biology, University of Copenhagen, Denmark. The PhD position concerns protein structure prediction, and will be in the Structural Bioinformatics group of Associate professor Thomas Hamelryck. The group is an integrated part of the Bioinformatics Center, which is headed by Professor Anders Krogh, employs around sixty scientists (including PhD students) and focuses on non-coding RNA, eukaryotic gene regulation and protein structure prediction. The center provides a modern, pleasant, international working environment with excellent modern facilities, in the heart of Copenhagen.
The project will be supervised by Associate Professor Thomas Hamelryck.

The protein folding problem is of enormous practical, theoretical and medical importance - and in addition forms a fascinating intellectual challenge. The aim of this project is to develop and implement a probabilistic method to infer the structure of proteins, building on various probabilistic models of protein structure developed by the Hamelryck group. The method will also take the dynamic nature of proteins into account, and involves a close collaboration with the statistics department at the university within the interdisciplinary project "Dynamical Systems: Mathematical Modeling and Statistical Methods for the Social, Health, and Natural Sciences" (http://dsin.ku.dk/).

Qualifications
Knowledge of programming (C++) and statistics or machine learning. Knowledge of biology, physics or biophysics is a plus, but not a requirement.

The deadline for applications is June 15, 2014

More at : https://job.jobnet.dk/CV/FindJob/details.aspx/3695051%20

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!

STRUM: structure-based prediction of protein stability changes upon single-point mutation

BioStar — Mon, 10 Sep 2018 13:21:49 -0500

STRUM is a method for predicting the fold stability change (ΔΔG) of protein molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy changes on a variety of features at different levels of sequence and structure properties. The unique characteristics of STRUM is the combination of sequence profiles with low-resolution structure models from protein structure prediction, which helps enhance the robustness and accuracy of the method and make it applicable to various protein seqences, including those without experimental structures

Address of the bookmark: https://zhanglab.ccmb.med.umich.edu/STRUM/

pybedtools

Shruti Paniwala — Wed, 20 Aug 2014 01:03:41 -0500

pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs (https://github.com/arq5x/bedtools), which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python. See full online documentation, including installation instructions, at http://pythonhosted.org/pybedtools/.

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

PPAI: a web server for predicting protein-aptamer interactions

Jit — Fri, 12 Jun 2020 07:26:23 -0500

PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI

Address of the bookmark: http://39.96.85.9/PPAI/

Roderic Guigó Lab

Mon, 01 Sep 2014 17:13:00 -0500

Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc…). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences. Our group also actively participates in the analysis of many eukaryotic genomes and it in involved in the NIH-funded ENCODE project. Furthermore we are members of two large cancer-studies consortia (chronic lymphocytic leukemia "CLL" and Breast Cancer -Hospital del Mar/CRG/Roche-).

More at http://big.crg.cat/computational_biology_of_rna_processing

Amino Acid Flash Tutorial

Jit — Mon, 11 Aug 2014 08:58:17 -0500

Protein is a part of every cell in your body, and no other nutrient plays as many different roles in keeping you alive and healthy. Protein is the building block of our body, and amino acids are the main areas of interest. We have emphasized on all 20 amino acids in this documentary movie. This documentary has been developed that emphasize on chemical structure, chemical formula, IUPAC name and other detail information of all 20 amino acids with the voice, picture with interactive button. This will be helpful for the entire biology and bioinformatics student.

How to run?

You need to install flash player or open it with web browser ( I guess you have installed flash plugin) to play.

Comment below if you like it. Thanks

Bioinformatics JRF/SRF position at IARI

Thu, 04 Sep 2014 04:14:01 -0500

DIVISION OF NEMATOLOGY
INDIAN AGRICULTURAL RESEARCH INSTITUTE
NEW DELHI 110012
Applications are invited for the posts of one Junior
Research Fellow and one RA in the DBT funded project entitled “ Plant parasitic nematode genome informatics - insilico resource development”. The project is for a period of three years.

Essential qualifications for JRF
: M. Sc. in Bioinformatics with experience in Proteomics, genomics and structural biology. Knowledge of programming language, pearl and database – HTML, CSS,php and Java script.
Essential qualifications for Research Associate:
MSc/MTech in Bioinformatics with three years experience or Ph.D in Bioinformatics with experience in proteomics, genomics and structural biology. Knowledge of programming language, perl and database
– HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm designing.
Age limit : 35 years maximum (5 year relaxation for SC/ST and women candidates)
Emoluments:
JRF: 16,000 + 30% HRA
.
Res Assoc: Rs22,000 + 30% HRA
The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.
Interested candidates
should send the duly filled application forms (format in the following page ) so as to reach on or before 20.9.2014 along with all the relevant documents.

More at http://www.iari.res.in/files/JRF_RA-03092014-20140903-135319.pdf

Protein Subcellular Localization Prediction

Poonam Mahapatra — Thu, 01 Mar 2018 06:20:47 -0600

Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and laborious experimental methods.

http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi

Address of the bookmark: https://abi.inf.uni-tuebingen.de/Research/Systems%20Biology/protein-subcellular-localization