BOL: Related items

Bioinformatics Algorithms (Part 1) with Pavel Pevzner, Phillip E. C. Compeau,

Mon, 30 Sep 2013 11:34:09 -0500

The course Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, and Nikolay Vyahhi from University of California, San Diego will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/bioinformatics.

Bioinformatics algorithms tutorials

John Parker — Tue, 24 Jun 2014 00:10:45 -0500

Useful bioinformatics tutorial, such as

De Bruijn Graphs for NGS Assembly
Algorithms for PacBio Reads
Software and Hardware Concepts for Bioinformatics
Finding us in Homolog.us (Search Algorithms)
NGS Genome and RNAseq Assembly - a Hands on Primer
Introduction to PERL, Python, R and C/C++ for Bioinformatics

Address of the bookmark: http://www.homolog.us/Tutorials/

Tetra-Nucleotide Analysis

Jit — Thu, 04 May 2017 05:07:41 -0500

A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the information of whole genome, it is evident that it cannot replace other alignment-based phylogenetic methods such as OrthoANI or 16S rRNA phylogeny. However, TNA can be useful for phylogenetic characterization when whole genome or 16S rRNA gene information is not available. For example, a partial genomic fragment obtained from a metagenome can be identified by TNA (Teeling et al., 2004). TNA is also fast enough that it can be used as a search engine against a large genome database.

Address of the bookmark: https://chunlab.wordpress.com/tetra-nucleotide-analysis/

Algorithms for DNA Sequencing (course offered each month)

Rahul Agarwal — Sun, 26 Jul 2015 01:57:02 -0500

"We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets."

Source : https://www.coursera.org/course/ads1

Address of the bookmark: https://www.coursera.org/course/ads1

Pevzner Lab !

Thu, 02 Nov 2023 05:39:26 -0500

The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.

https://bioalgorithms.ucsd.edu/research4.html

Bioinformatics Programme Officer @ International Centre for Genetic ICGEB Engineering and Biotechnology

Fri, 23 Nov 2018 03:50:16 -0600

The following vacancies are available in the DBT Apex Biotechnology Information project at ICGEB, New Delhi, India. These positions are available for a period of approx. two years, however, initial appointment offer will be for 6 months, which will be extended based on performance of work. Salaries will be offered as per DBT, educational qualification and experience. Depending on requirements, selected candidates may be required to work on location from the Department of Biotechnology, New Delhi. Shortlisted candidates will be invited for an interview at ICGEB. Only the selected candidates will be informed individually. No TA/DA or accommodation will be offered to the candidates attending the interview.

4 Programme Officer 1
5 Technical Research Assistant 1

Minimum Educational Qualification, desirable experience and expected duties:

4: The applicants should be Postgraduates with experience in Data collection and Statistics, especially in Biotechnology-related data.

Expected duties: Collection of Biotechnology related information from India, to facilitate the Apex BTIC experts committee review of programmes at centres and R&D programs funded by DBT.

5: The applicants should be Postgraduates in Science with experience in Bioinformatics-related projects.
Expected duties: The candidates will assist the senior staff of the centre in daily activities and help in the preparation of the Annual Training Calendar, seminar and training podcasts/videos, repository of training material and Apex BTIC Newsletter.

Interested candidates should submit their full, updated Curriculum Vitae with a detailed description of relevant experience, along with two references by December 14th, 2018, addressed to, The Chairperson, DBT- Apex BTIC, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, Email: abtic@icgeb.res.in, kindly write “Application for DBT Apex BTIC vacancy” in the subject of the email or envelope, if sending by post.

Advertisement: http://www.icgeb.org/tl_files/Vacancies/dbt-abtic-vac-annmntrevsk.pdf

GPOPSIM: a simulation tool for whole-genome genetic data

Jit — Wed, 17 Jan 2018 03:47:46 -0600

GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.

Address of the bookmark: https://github.com/SCAU-AnimalGenetics/GPOPSIM

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker