A repository for the lessons and tutorials for the Functional Annotation TOPIC channel of the BVCN
This BVCN topic will cover:
- how to predict opening reading frames for all three domains of life
- the methodologies used to assign functions to proteins
- the intricacies of the specific tools and databases that can used for varying levels of specificity
Date posted: 9 April 2020
Author(s): Dr. Benjamin Tully
Instructor(s): Dr. Benjamin Tully
- Tools for predicting open reading frames for Bacteria and Archaea
- Tools for predicting open reading frames for Eukaryotes
- Converting open reading frames to predicted proteins
Date posted: 9 April 2020
Author(s): Dr. Benjamin Tully
Instructor(s): Dr. Benjamin Tully
- Use Prodigal to predict microbial proteins
Content | Video presentation |
Primary tools/programs used:
Date posted: 18 April 2020
Author(s): Dr. Benjamin Tully
Instructor(s): Dr. Benjamin Tully
- Difference between homolog and ortholog?
- Tools for homology based functional annotation
Date posted: 9 April 2020
Author(s): Dr. Benjamin Tully
Instructor(s): Dr. Benjamin Tully
- Use BLAST+ and DIAMOND
- Interpret similarity based results
Content | Video presentation |
Primary tools/programs used:
Date posted: 1 May 2020
Author(s): Dr. Benjamin Tully, Dr. Adelaide Rhodes
Instructor(s): Dr. Benjamin Tully
- How do position-sensitive models work?
- How to use a position-sensitive model to interpret function
Date posted: 1 May 2020
Author(s): Dr. Benjamin Tully, Dr. Adelaide Rhodes
Instructor(s): Dr. Benjamin Tully
- Use HMMER
- Interpret HMM search results
Content | Video presentation |
Primary tools/programs used:
Date posted: 5 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Describe the process for making HMM to detect iron-related proteins
- How FeGenie works
Date posted: 5 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Demonstration of how FeGenie identifies iron-related proteins
Content | Video presentation |
Primary tools/programs used:
Date posted: 7 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Profiling datasets using HMMs
- HMMER web interface
- Getting HMMs from Pfam and TIGRFAMS
- MagicLamp introduction
- Make your own genie with HmmGenie
Date posted: 7 May 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Demonstration of how MagicLamp profiles datasets with various HMM sets
- Demontration on how to make your own HMMs
- Demontration on how to use your own HMM sets with HmmGenie
Content | Video presentation 1 | Video presentation 2
tutorial 1:
tutorial 2:
Primary tools/programs used:
Date posted: 22 May 2020
Author(s): Arkadiy Garber & Ben Tully
Instructor(s): Ben Tully & Arkadiy Garber
- Introduction to KEGG
- KEGG online interface
- GhostKOALA and BlastKOALA
- GHOSTX
- KOALA-formatter
- KofamKoala
- KEGG-Decoder
Date posted: 22 May 2020
Author(s): Ben Tully
Instructor(s): Ben Tully
- Demonstration of how to use KEGG-Decoder
Content | Video presentation |
Primary tools/programs used:
Date posted: 3 August 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Introduction to Secondary Metabolites
- Antimicrobials
- Siderophores
- Introduction to AntiSMASH
- Overview of AntiSMASH web interface
Date posted: 3 August 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Demonstration of how to use standalone command-line AntiSMASH
Content | Video presentation |
Primary tools/programs used:
Date posted: 14 October 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Introduction to pseudogenes
- Pseudofinder algorithm overview
- Pseudofinder output
Date posted: 14 October 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Demonstration of how to use Pseudofinder
Content | Video presentation |
Primary tools/programs used: