BOL: Related items

Efficient genome searching with Biostrings and the BSgenome data package

Aasha — Mon, 07 Mar 2016 05:18:06 -0600

Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

PhD at INSTITUTE OF LIFE SCIENCES, Bhubaneswar

Mon, 30 May 2016 03:36:04 -0500

INSTITUTE OF LIFE SCIENCES

Bhubaneswar 751023

Advt No. 07/2016

Institute of Life Sciences (ILS), Bhubaneswar, an autonomous Institute of the Department of Biotechnology, Ministry of Science & Technology, Government of India engaged in advanced research invites applications from Indian nationals for the Ph.D. program. The main focus of the projects will be computational biology in the following areas.

S. No. Area of Research Principal investigator

1. Computational Cancer Biology Dr. Anshuman Dixit

2. Immunogenomics & Systems Biology Dr. Sunil Kumar Raghav

3. Chromatin remodeling and hematopoiesis Dr. Punit Prasad

Candidates are strongly encouraged to visit ILS webpage for detailed information, regarding the research activities of the above mentioned scientists.

Essential Qualifications:

(a) Eligibility: M.Sc., M.V.Sc., M.Pharm., M.S. Pharma. (with NET/GATE/GPAT/BINC/any other equivalent national level exam) or M.Tech with minimum of 60% marks (or equivalent grade point). Those awaiting final result may also apply.

Applications received after the last date will not be accepted. The envelope should clearly be superscribed with “Application for Ph.D. program (computational biology)”. Short-listed candidates selected for the interview will be published in the Institute website (www.ils.res.in).

Application Fees: Applicants except SC/ST candidates are required to send a non-refundable D.D. for Rs.100/- in favour of “Director, Institute of Life Sciences, Bhubaneswar” payable at Bhubaneswar along with duly filled-in application form by the date mentioned below. Director, ILS reserves the right to withdraw the procedure without assigning any reasons thereof.

Important dates: 

Last date of receiving applications: 24th June 2016 

Date of display of short-listed candidates and instructions on the Institute website: 30th June 2016 

Date of interview: The interview will be organized on 25th July 2016

Advertisement: https://www.ils.res.in/wp-content/uploads/2016/05/advt07-16.pdf

Awesome bioinformatics pipelines !

Jitendra Prajapati — Wed, 30 Mar 2016 21:50:41 -0500

A curated list of awesome pipeline toolkits ...

https://github.com/pditommaso/awesome-pipeline

Address of the bookmark: https://github.com/pditommaso/awesome-pipeline

AccNET

Jitendra Narayan — Fri, 07 Oct 2016 05:22:11 -0500

AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures.

More at https://www.youtube.com/watch?v=vdGuy1GAJrQ

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

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

TGNet

Shruti Paniwala — Wed, 24 Aug 2016 05:36:36 -0500

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis.

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

Gene Finding and Predictions

Poonam Mahapatra — Fri, 26 Aug 2016 07:26:27 -0500

In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (protein and cDNA sequences) methods will be employed in order to improve the ab initio results. Weak conservation of Start codons will lead to wrong prediction of initial exons in most cases.

http://genome.crg.es/courses/Bioinformatics2003_genefinding/

Address of the bookmark: http://genome.crg.es/courses/Bioinformatics2003_genefinding/

Sushi: An R/Bioconductor package for visualizing genomic data

Jit — Wed, 31 Aug 2016 08:29:12 -0500

Sushi: An R/Bioconductor package for visualizing genomic data

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

R-chie

Jit — Thu, 01 Sep 2016 11:47:24 -0500

R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation information.
R4RNA is the R package powering R-chie, available for download and local use for more customized figures and scripting.

http://www.e-rna.org/r-chie/plot.cgi?eg=single

Address of the bookmark: http://www.e-rna.org/r-chie/plot.cgi?eg=single

Assembly tutorial PPT

Jit — Wed, 07 Sep 2016 03:12:53 -0500

Saved Cornell University assembly workshop PPT.

Reference:

http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf