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Scientific topics: Sequence analysis 


Bioinformatics - Food Detective: a Practical Guide

This Practical Guide introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help de- tect food fraud. Analyses...

Scientific topics: Sequence analysis, Community profiling

Keywords: Basic bioinformatics, Bioinformatics schools, Dna barcoding, Food fraud, Sequence analysis, Sequence database searching, Species identification, Training material

Bioinformatics - Food Detective: a Practical Guide https://tess.elixir-europe.org/materials/bioinformatics-food-detective-a-practical-guide This Practical Guide introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help de- tect food fraud. Analyses are run online using sequence data from the 4273pi project website: 4273pi.org. This Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how to identify different spe- cies based on their specific DNA sequences – their ‘barcodes’. On reading the Guide and completing the exercises, you will be able to: i) explain what is meant by DNA barcoding; ii) search biological sequence databases using the online program BLAST; iii) judge the reliability of database-search results in terms of their statistical significance; and iv) evaluate the biological implications of search results with reference to food safety. Sequence analysis Community profiling Basic bioinformatics, Bioinformatics schools, Dna barcoding, Food fraud, Sequence analysis, Sequence database searching, Species identification, Training material 2020-06-23
Bioinformatics - the Power of Computers in Biology: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in...

Scientific topics: Sequence analysis

Keywords: Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials

Bioinformatics - the Power of Computers in Biology: A Practical Guide https://tess.elixir-europe.org/materials/bioinformatics-the-power-of-computers-in-biology-a-practical-guide This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273π variant of Linux (4273pi.org). Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to: i) search biological sequence databases using the online program BLAST, and navigate GenPept sequence records; ii) execute some basic Linux commands to perform a set of simple file-manipulation tasks; iii) perform BLAST searches via the Linux command line; and iv) evaluate the biological implications of search results, with reference to mutations and function. Sequence analysis Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials 2019-06-08
Basic bioinformatics concepts, databases and tools

During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling...

Scientific topics: Sequence analysis

Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/materials/basic-bioinformatics-concepts-databases-and-tools During this 3-day introduction to bioinformatics, BITS will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune it in order the get the most out of your analysis. Sequence analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/tgac_seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data analysis for plant species data Data quality checks Estimation of reproducibility Batch effects Statistical concepts Importance of standards Data formats Data integration What will I learn? To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions Identify key challenges, opportunities and bottlenecks Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics Sequence analysis Plant biology Database management Bioinformatics Ngs, Ngs bioinformatics, Plants bioinformatics PhD students plant researchers post-docs 2015-06-22 2017-10-09