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Keywords: Protein sequence analysis 


A Critical Guide to InterPro

This Critical Guide in the Introduction to Bioinformatics series provides an introduction to the InterPro database, the largest, most comprehensive, integrated protein family database in the world. The rationale for creating the resource, the nature of its contributing databases and the kinds of...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis

A Critical Guide to InterPro https://tess.elixir-europe.org/materials/a-critical-guide-to-interpro This Critical Guide in the Introduction to Bioinformatics series provides an introduction to the InterPro database, the largest, most comprehensive, integrated protein family database in the world. The rationale for creating the resource, the nature of its contributing databases and the kinds of information they provide are discussed, and the role of InterPro in protein classification and function-annotation projects is outlined. Specifically, this Guide introduces the principal components of the InterPro database, the differences between them, and how their integration creates a resource whose diagnostic power is greater than the sum of its parts. On reading this Guide, users will be able to: i) explain how protein family databases are used to help annotate uncharacterised protein sequences; ii) identify InterPro’s constituent data resources and explain the main methods that underpin them; iii) search InterPro using keywords and full sequences; iv) analyse and interpret search results in terms of protein family hierarchies, their structural domains and functional features; and v) track the provenance of InterPro’s annotations. Database management Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis Beginners 2018-09-08
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies https://tess.elixir-europe.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Understanding Multiple Sequence Alignments - Lecture Handouts & Utopia Hands-On

This presentation aims to provide a basic understanding of the range of contexts in which protein sequence alignments are used and are useful, focusing on the importance of sequence similarities and differences, and what they tell us. Overall, the objective is to offer different perspectives and...

Keywords: Multiple sequence alignment, Protein sequence analysis, Sequence analysis

Understanding Multiple Sequence Alignments - Lecture Handouts & Utopia Hands-On https://tess.elixir-europe.org/materials/understanding-multiple-sequence-alignments-lecture-handouts-utopia-hands-on This presentation aims to provide a basic understanding of the range of contexts in which protein sequence alignments are used and are useful, focusing on the importance of sequence similarities and differences, and what they tell us. Overall, the objective is to offer different perspectives and insights into the meaning of alignments, and to convey an understanding of the use of metaphor and its role in interpreting alignments. The talk is accompanied by a hands-on practical analysis using the Utopia sequence analysis suite. Multiple sequence alignment, Protein sequence analysis, Sequence analysis Biomedical researchers Life Science Researchers Postgraduate students 2013-12-17 2017-10-09
Bioinformatics: Gene-protein-structure-function

This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...

Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast

Bioinformatics: Gene-protein-structure-function https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The presentation concludes with an analysis of 'expert' systems and integrated approaches (GeneQuiz, MAGPIE, InterPro, etc.), and dispels the commonly held notion that one database and/or one analysis tool is best. Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
InterPro: An introduction

This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose. 

Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis

InterPro: An introduction https://tess.elixir-europe.org/materials/interpro-an-introduction This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.  Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
PRINTS: A protein family database with a difference

A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...

Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis

PRINTS: A protein family database with a difference https://tess.elixir-europe.org/materials/prints-a-protein-family-database-with-a-difference A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to demonstrate the importance of understanding how to interpret the results of different sequence analysis methods and, crucially, the differences between them, and the added value that fingerprints bring. Functional diagnosis, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09