Genome Annotation

🛠️ Comparison of two annotation tools: Helixer and Braker3

2025-06-20T14:13:33+00:00

The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.

📚 Comparison of two annotation tools - Helixer and Braker3

2025-06-20T14:13:33+00:00

Annotating the eukaryotic genome represents a somewhat more complex challenge than that of prokaryotes, mainly due to the generally larger size of eukaryotic genomes and their greater number of genes. This annotation can be carried out at different levels of precision, ranging from simple identification of coding and non-coding parts to detailed structural labeling, including for example the precise location of exons, introns and other regulatory elements.

🛠️ Genome annotation with Braker3

2025-03-17T10:24:07+00:00

This workflow uses Braker3 to annotate a genome.

📚 Genome annotation with Braker3

2025-03-17T10:24:07+00:00

🎥 Recording of Identification of AMR genes in an assembled bacterial genome

2024-09-24T00:00:00+00:00

A 26M long recording is now available.

🎥 Recording of Long non-coding RNAs (lncRNAs) annotation with FEELnc

2024-09-11T00:00:00+00:00

A 11M long recording is now available.

🎥 Recording of Bacterial Genome Annotation

2024-09-02T00:00:00+00:00

A 44M long recording is now available.

🛠️ annotation_helixer

2024-08-21T15:23:33+00:00

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

📚 Genome annotation with Helixer

2024-08-21T15:23:33+00:00

Annotating the eukaryotic genome represents a somewhat more complex challenge than that of prokaryotes, mainly due to the generally larger size of eukaryotic genomes and their greater number of genes, but also to the complexity of eukaryotic genes structure (e.g. exons and Untranslated region (UTR)). This annotation can be carried out at different levels of precision, ranging from simple identification of coding and non-coding parts to detailed structural labeling, including for example the precise location of exons, introns and other regulatory elements.

📰 GTN ❤️ GMOD

2024-02-29T00:00:00+00:00

Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.

🛠️ Gene Cluster Product Similarity Search

2024-02-21T14:08:32+00:00

🛠️ Bacterial Genome Annotation

2024-02-01T10:04:54+00:00

Bacterial Genome Annotation

📚 Bacterial Genome Annotation

2024-02-01T10:04:54+00:00

After sequencing and assembly, a genome can be annotated. It is an essential step to describe the genome.

🛠️ mrsa AMR gene detection

2024-01-23T16:20:06+00:00

Identification of AMR genes in an assembled bacterial genome

📚 Identification of AMR genes in an assembled bacterial genome

2024-01-23T16:20:06+00:00

Antimicrobial resistance (AMR) is a global phenomenon with no geographical or species boundaries, which poses an important threat to human, animal and environmental health. It is a complex and growing problem that compromises our ability to treat bacterial infections.

🛤️ Genome annotation for prokaryotes

2023-06-27T16:08:20+00:00

Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo.

🛤️ Genome annotation for eukaryotes

2023-06-27T16:08:20+00:00

Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.

🎥 Recording of Genome annotation with Funannotate

2023-05-12T00:00:00+00:00

A 1H10M long recording is now available.

🎥 Recording of Masking repeats with RepeatMasker

2023-05-10T00:00:00+00:00

A 18M long recording is now available.

🛠️ Long non-coding RNAs (lncRNAs) annotation with FEELnc

2022-09-23T14:33:06+00:00

Long non-coding RNAs (lncRNAs) annotation with FEELnc

📚 Long non-coding RNAs (lncRNAs) annotation with FEELnc

2022-09-23T14:33:06+00:00

Messenger RNAs (mRNAs) are not the only type of RNAs present in organisms (like mammals, insects or plants) and represent only a small fraction of the transcripts. A vast repertoire of small (miRNAs, snRNAs) and long non-coding RNAs (lncRNAs) are also present. Long non-coding RNAs (LncRNAs) are generally defined as transcripts longer than 200 nucleotides that are not translated into functional proteins. They are important because of their major roles in cellular machinery and their presence in large number. Indeed, they are notably involved in gene expression regulation, control of translation or imprinting. Statistics from the GENCODE project reveals that the human genome contains more than 19,095 lncRNA genes, almost as much as the 19,370 protein-coding genes.

🛠️ Comparative gene analysis

2022-09-08T13:09:47+00:00

Workflows for comparison of genes in annotated genomes

📚 Comparative gene analysis in unannotated genomes

2022-09-08T13:09:47+00:00

Despite the rapidly increasing number of fully assembled genomes few genomes are well annotated. This is especially true for large eukaryotic genomes with their complex gene structure and abundance of pseudogenes. And of course do not forget about the Murthy’s law: if you are interested in a particular gene the chances are that it will not be annotated in your genome of interest. In this tutorial we will demonstrate how to compare gene structures across a set of vertebrate genomes. So …

📚 Refining Genome Annotations with Apollo (eukaryotes)

2022-08-22T19:31:27+00:00

After automatically annotating your genome using Funannotate or Maker for example, it is important to visualize your results so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is most often done as part of a group, smaller organisms may be annotated individually though.

🛠️ Functional annotation

2022-07-20T18:34:12+00:00

Functional annotation of protein sequences

📚 Functional annotation of protein sequences

2022-07-20T18:34:12+00:00

When performing the structural annotation of a genome sequence, you get the position of each gene, but you don’t have information about their name of their function. That’s the goal of functional annotation.

🎥 Recording of Introduction to CRISPR screen analysis

2022-03-10T00:00:00+00:00

A 3M long recording is now available.

🎥 Recording of CRISPR screen analysis

2022-03-10T00:00:00+00:00

A 45M long recording is now available.

🖼️ Introduction to CRISPR screen analysis

2022-03-07T16:34:05+00:00

What is CRISPR?

🎥 Recording of Masking repeats with RepeatMasker

2022-03-03T00:00:00+00:00

A 16M long recording is now available.

🎥 Recording of Genome annotation with Funannotate

2022-03-03T00:00:00+00:00

A 1H10M long recording is now available.

📰 New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate

2021-12-01T00:00:00+00:00

We have just finished a new collection of training material for genome assembly and annotation! You now have access to slides and tutorials, focused on the complete analysis of the genome of a fungus species (Mucor mucedo).

🛠️ RepeatMasker

2021-11-29T13:29:30+00:00

Masking repeats in a genome using RepeatMasker

🛠️ Funannotate

2021-11-29T13:29:30+00:00

Structural and functional genome annotation with Funannotate

📚 Masking repeats with RepeatMasker

2021-11-29T13:29:30+00:00

When you assemble a new genome, you get its full sequence in FASTA format, in the form of contigs, scaffolds, or even whole chromosomes if you are lucky. However genomes, in particular for eukaryote organisms, contain a varying but significant proportion of repeated elements all along the sequence. These elements belong to different classes, including:

📚 Genome annotation with Funannotate

2021-11-29T13:29:30+00:00

Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved.

🛠️ Workflow constructed from history 'CRISPR tutorial Kenji'

2021-10-15T07:01:26+00:00

CRISPR screen analysis

📚 CRISPR screen analysis

2021-10-15T07:01:26+00:00

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system is a bacterial immune system that has been modified for genome engineering. This groundbreaking technology resulted in a Nobel Prize for Emmanuelle Charpentier and Jennifer Doudna in 2020 (Uyhazi and Bennett 2021). CRISPR consists of two components: a guide RNA (gRNA) and a non-specific CRISPR-associated endonuclease (Cas9). The gRNA is a short synthetic RNA composed of a scaffold sequence necessary for Cas9-binding (trRNA) and ~20 nucleotide spacer or targeting sequence which defines the genomic target to be modified (crRNA). Cas9 induces double-stranded breaks (DSB) within the target DNA. The resulting DSB is then repaired by either error-prone Non-Homologous End Joining (NHEJ) pathway or less efficient but high-fidelity Homology Directed Repair (HDR) pathway. The NHEJ pathway is the most active repair mechanism and it leads to small nucleotide insertions or deletions (indels) at the DSB site. This results in in-frame amino acid deletions, insertions or frameshift mutations leading to premature stop codons within the open reading frame (ORF) of the targeted gene. Ideally, the end result is a loss-of-function mutation within the targeted gene; however, the strength of the knockout phenotype for a given mutant cell is ultimately determined by the amount of residual gene function.

🖼️ Refining Genome Annotations with Apollo

2021-06-04T16:47:17+00:00

Genome annotation

🛠️ Apollo Load Test

2021-06-04T09:17:20+00:00

Refining Genome Annotations with Apollo

📚 Refining Genome Annotations with Apollo (prokaryotes)

2021-06-04T09:17:20+00:00

After automatically annotating your genome using Prokka for example, it is important to visualize your results so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is most often done as part of a group, smaller organisms may be annotated individually though.

📰 New Tutorial: Genome Annotation with Apollo

2021-06-04T00:00:00+00:00

After two years, the Galaxy Genome Annotation team has finally finished their much awaited tutorial on doing Genome Annotation in Galaxy! Genome annotation is a time consuming and largely manual process as it requires the synthesis of a significant amount of varied information to make inferences, a process tha cannot be accomplished without an interactive editor. To support this, Apollo was deployed on UseGalaxy.eu. Over the past two years the GGA project has pushed forward apollo and tooling around it, and it finally culminates in this look at how to annotated your genomes in Apollo.

🎥 Recording of Refining Genome Annotations with Apollo

2021-02-15T00:00:00+00:00

A 5M long recording is now available.

🎥 Recording of Refining Genome Annotations with Apollo (prokaryotes)

2021-02-15T00:00:00+00:00

A 1H long recording is now available.

🎥 Recording of Genome annotation with Prokka

2021-02-15T00:00:00+00:00

A 3M long recording is now available.

🎥 Recording of Genome annotation with Prokka

2021-02-15T00:00:00+00:00

A 20M long recording is now available.

🛠️ GECKO pairwise comparison

2021-02-08T01:33:47+00:00

A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment

🛠️ CHROMEISTER chromosome comparison

2021-02-08T01:33:47+00:00

A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER

🖼️ High Performance Computing for Pairwise Genome Comparison

2021-02-08T01:33:47+00:00

What is sequence comparison?

📚 From small to large-scale genome comparison

2021-02-08T01:33:47+00:00

Sequence comparison is a core problem in bioinformatics. It is used widely in evolutionary studies, structural and functional analyses, assembly, metagenomics, etc. Despite its regular presence in everyday Life-sciences pipelines, it is still not a trivial step that can be overlooked. Therefore, understanding how sequence comparison works is key to developing efficient workflows that are central to so many other disciplines.

🛠️ Genome annotation with Maker (short)

2021-01-12T13:45:59+00:00

Genome annotation with Maker (short)

📚 Genome annotation with Maker (short)

2021-01-12T13:45:59+00:00

🛠️ Essential genes detection with Transposon insertion sequencing

2020-10-18T21:53:16+00:00

Essential genes detection with Transposon insertion sequencing

🖼️ Essential genes detection with Transposon insertion sequencing

2019-07-02T09:57:56+00:00

📚 Essential genes detection with Transposon insertion sequencing

2019-07-02T09:57:56+00:00

In microbiology, identifying links between genotype and phenotype is key to understand bacteria growth and virulence mechanisms, and to identify targets for drugs and vaccines. These analysis are limited by the lack of bacterial genome annotations (e.g. 30% of genes for S. pneumoniae are of unknown function) and by the fact that genotypes often arose from complex composant interactions.

🖼️ Introduction to Genome Annotation

2019-05-13T20:23:49+00:00

Genome Annotation

🛠️ Genome annotation with Maker

2018-09-24T16:21:32+00:00

Genome annotation with Maker

📚 Genome annotation with Maker

2018-09-24T16:21:32+00:00

🛠️ Genome Annotation with Prokka

2018-03-06T18:15:31+00:00

Genome annotation with Prokka

🖼️ Genome annotation with Prokka

2018-03-06T18:15:31+00:00

📚 Genome annotation with Prokka

2018-03-06T18:15:31+00:00

In this section we will use a software tool called Prokka to annotate a draft genome sequence. Prokka is a “wrapper”; it collects together several pieces of software (from various authors), and so avoids “re-inventing the wheel”.