BOL: Related items

33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014

Tue, 27 Aug 2013 10:37:08 -0500

RGCB is organizing the 33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014 with the theme "Discovery, Innovation and Translation in Cancer Research"

Kindly log on to conference website http://rgcb.res.in/IACR2014 for further details and timely updates and registration. We shall truly appreciate if the same be circulated among your friends, scholars and students encouraging them to participate in the meet.

http://210.212.237.38/iacrconference/

BioGPS

Anjana — Mon, 23 May 2016 03:15:46 -0500

A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.

http://biogps.org/#goto=welcome

Address of the bookmark: http://biogps.org/#goto=welcome

GeneBreak: a tool to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach

Jit — Sat, 01 Oct 2016 15:15:29 -0500

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).

Address of the bookmark: http://www.bioconductor.org/packages/release/bioc/html/GeneBreak.html

Understanding liftOver !

Rahul Nayak — Wed, 06 Jun 2018 10:00:20 -0500

LiftOver is a necesary step to bring all genetical analysis to the same reference build. LiftOver can have three use cases:

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

Run:

liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

The outformat is as follow:

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

For example:

If you liftOver chr4:6497-6497 from hg19 to GRch38 and it return "deleted in new".

It means chr4:6497-6497 is part of a genomic contig on hg19 that is not anymore mapped on GRch38 because the new assembly is now better built without including this contig.

Genomic Scientist at UDSC

Thu, 28 May 2015 19:14:23 -0500

Centre for Genetic Manipulation of Crop Plants

Department of Genetics

University of Delhi South Campus

NEW DELHI – 110 021

WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT

1 Research Scientist (RS) – 3

DBT, Ph. D.

Experience on DNA Markers, plant genome mapping and bioinformatics

Salary: 60,000 (Consolidated) + 5% annual increment

Date and time: 25.06.2015 at 10:30 AM

These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.

Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.

No TA/DA will be paid for attending the interview.

www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Rahul Nayak — Sun, 17 May 2020 10:27:44 -0500

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

Address of the bookmark: https://github.com/PapenfussLab/gridss

PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis

LEGE — Mon, 01 Sep 2025 01:18:10 -0500

This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.

Address of the bookmark: https://github.com/liviurotiul/PeGAS

SVfinder: Tool for detecting genomic rearrangement form DNA-seq data

Robert M Willioms — Thu, 14 Dec 2017 15:51:40 -0600

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

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

Bourque Lab

Mon, 14 Jan 2019 15:39:25 -0600

The goal of the lab is to understand mammalian genomes using comparative genomic and epigenomic analyses. Areas of interest include: the evolution of regulatory sequences, the role of transposable elements in gene regulation and the impact of genome rearrangements in evolution and cancer.

As a computational genomicists our work involves examining billions of DNA base pairs and interpreting how variation impacts basic biology and disease. We develop computational methods and resources for the functional annotation of genomes with a special emphasis on sequencing-based assays (e.g. ChIP-seq, RNA-Seq, exome- and whole-genome sequencing, single-cell analysis).

http://www.computationalgenomics.ca