BOL: Related items

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

A comprehensive atlas of human gene activity released !!!

Abhimanyu Singh — Tue, 02 Sep 2014 14:20:24 -0500

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

We are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles. This is a major advance that will greatly increase our ability to understand the causes of disease across the body.

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches” — called “promoters” and “enhancers” — are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

Referene : www.kurzweilai.net/first-comprehensive-atlas-of-human-gene-activity-released

Primer BLAST !

BioStar — Tue, 28 Apr 2020 00:28:49 -0500

BLAST team added a new feature (Max 3' match), shown in Figure 1, to Primer-BLAST that limits the length of 3' exon matches when designing exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in expression assays. See the NCBI Insights post (https://go.usa.gov/xvUT4) for more details.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

Which of the following programming language is best for a bioinformatics beginner?

Manisha Mishra — Thu, 04 Sep 2014 07:51:16 -0500

I will be doing NGS in the course of my research work and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Recommendations welcomed. Which languages would you recommend to a student wishing to enter the world of bioinformatics?

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

Research Scientist – Bioinformatics at Sidra Medical and Research Center

Wed, 10 Sep 2014 14:35:35 -0500

Sidra Medical and Research Center(Doha, Qatar) is looking for talented Research Scientists (Bioinformatics / NGS Data Analysis).

Research Scientists within the Bioinformatics Program are involved in research related to cutting edge genomics and analysis of omics data. The research will utilize concepts, theories and best practices obtained from bioinformatics discipline and applied to biological and other biomedical data for analysis. The role may also involve designing databases, algorithm and/or computation methods for analyzing genomics and other omics data. The scientist will be working closely with the Translational Medicine Program within a state-of-the art research setting.

Please check the details of the opening and apply here: http://careers.sidra.org/sidra/Vacan...acancyID=60181

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

INTERNSHIP @ NIPGR

Sat, 13 Sep 2014 16:02:35 -0500

Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).

About National Institute Of Plant Genome Research (NIPGR) http://www.nipgr.res.in/

The National Institute of Plant Genome Research is an autonomous institution supported by the Department of Biotechnology, Government of India. It is committed to make the institute a premier Institution for plant genomic research in the country. It was established to contribute in the achievement of such hopes as a part of national effort for meeting the challenges in the midst of fast pace of international genomic research and grasping of opportunities on long-term basis.

About the Internship:

The selected intern(s) will work in the area of in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Who can apply:

Students currently pursuing the final year of Masters Degree (or equivalent) in Bioinformatics/Biotechnology with strong interest in Computational Biology and First class/division throughout academic career may apply.

DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms

Neel — Wed, 25 Nov 2020 19:51:38 -0600

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

Address of the bookmark: http://www.ub.edu/dnasp/

Java utilities for Next Generation Sequencing by Pierre Lindenbaum

Robert M Willioms — Mon, 15 Sep 2014 17:24:49 -0500

Java utilities for Bioinformatics

https://github.com/lindenb/jvarkit

Address of the bookmark: https://github.com/lindenb/jvarkit