The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

The postdoc will join our efforts to extend our methods repertoire to accurately detect additional types of genomic changes, to adopt them to other taxonomic groups, and to apply them on a large-scale to existing and numerous newly-sequenced genomes generated by us and our TBG collaborators.

Candidate requirements
· PhD degree in bioinformatics / computational biology, genomics or a related area

· a strong publication record

· excellent programming skills in a Linux environment as well as experience with shell scripting and Unix tools

· previous experience in large-scale comparative genomic data analysis is an advantage.

More at https://www.lifescience.net/jobs/71529/postdoc-mfd-comparative-genomics/

What is Bacterial Comparative Genomics?

Comparative genomics involves the systematic comparison of genomes across different bacterial species or strains. This approach allows scientists to:

• Identify conserved and unique genes.

• Explore genetic determinants of pathogenicity.

• Understand bacterial evolution and phylogenetics.

• Investigate horizontal gene transfer and its role in antibiotic resistance.

Bioinformatics is central to these analyses, enabling the processing and interpretation of large-scale genomic data.

Key Steps in Bacterial Comparative Genomics

1. Genome Sequencing and Assembly: The process begins with obtaining high-quality bacterial genome sequences. Advances in next-generation sequencing (NGS) technologies have made it faster and more affordable to sequence bacterial genomes. Tools such as SPAdes and Velvet are commonly used for genome assembly.

2. Genome Annotation: Annotating a genome involves identifying genes, regulatory elements, and other genomic features. Automated tools like Prokka and RAST provide functional annotations, allowing researchers to predict the roles of genes and proteins.

3. Genome Alignment: Aligning genomes is crucial for identifying conserved regions, single-nucleotide polymorphisms (SNPs), and structural variations. Tools like Mauve and progressiveMauve are commonly employed for whole-genome alignments.

4. Comparative Analyses:

   • Core and Pan-genome Analysis: The core genome consists of genes shared across all strains of a species, while the pan-genome includes all genes found in any strain. Software like Roary and BPGA can perform core and pan-genome analyses.

   • Phylogenetic Analysis: Comparative genomics often involves reconstructing evolutionary relationships. Tools such as MEGA and IQ-TREE facilitate phylogenetic tree construction based on genomic data.

   • Functional Enrichment Analysis: To understand the biological significance of unique or shared genes, functional enrichment analysis using databases like GO (Gene Ontology) and KEGG is essential.

Here are some additional bioinformatics tools that can aid bacterial comparative genomics:

• OrthoFinder: For accurate ortholog identification across multiple genomes.

• PanOCT: Specifically designed for pan-genome clustering and annotation.

• FASTANI: A tool for calculating Average Nucleotide Identity (ANI) for microbial genome comparisons.

• CIRCOS: For visually comparing genomic data through circular genome plots.

• Galaxy Platform: A user-friendly web-based platform offering numerous genomic analysis tools.

• BLAST: Essential for sequence alignment and similarity searches.

• PhyloSift: Focused on phylogenetic analysis of microbial genomes using marker genes.

These tools, in combination with the methods discussed, provide a robust framework for conducting comprehensive comparative genomic studies.

Applications of Bacterial Comparative Genomics

1. Understanding Pathogenicity: Comparative genomics helps identify virulence factors that distinguish pathogenic strains from non-pathogenic relatives. For instance, comparing genomes of Escherichia coli strains has revealed key genetic determinants of pathogenicity in enterohemorrhagic strains.

2. Antibiotic Resistance Research: The spread of antibiotic resistance genes through horizontal gene transfer is a major global concern. Comparative analyses can trace the origins and dissemination of resistance genes, aiding in the development of countermeasures.

3. Microbial Ecology and Evolution: By studying genomic variations, researchers can understand how bacteria adapt to different environments. This is particularly relevant for extremophiles and symbiotic bacteria.

4. Vaccine Development: Identifying conserved antigens across pathogenic strains is critical for vaccine design. Comparative genomics has been instrumental in developing vaccines against pathogens like Neisseria meningitidis.

5. Biotechnology Applications: Comparative studies can uncover unique metabolic pathways in bacteria, paving the way for applications in bioremediation, synthetic biology, and industrial microbiology.

Challenges in Bacterial Comparative Genomics

While the field has made significant strides, several challenges remain:

• Data Overload: The rapid growth of sequencing data requires robust computational infrastructure and efficient algorithms.

• Genome Plasticity: High rates of horizontal gene transfer and genome rearrangements in bacteria complicate comparative analyses.

• Annotation Accuracy: Automated annotation tools are not infallible, and manual curation is often needed for high-confidence results.

• Interpreting Non-Coding Regions: Understanding the functional significance of non-coding genomic regions remains a challenge.

Future Directions

The integration of bacterial comparative genomics with other ‘omics’ approaches—such as transcriptomics, proteomics, and metabolomics—promises a more comprehensive understanding of bacterial biology. Additionally, advancements in machine learning and artificial intelligence are likely to further enhance bioinformatics analyses, enabling the prediction of complex phenotypes from genomic data.

Conclusion

Bacterial comparative genomics, driven by bioinformatics, continues to unravel the complexities of bacterial life. From combating antibiotic resistance to uncovering the secrets of microbial evolution, this interdisciplinary field holds immense potential for addressing pressing challenges in microbiology and beyond. As technology advances, so too will our ability to harness the power of comparative genomics for scientific and societal benefit.

Tutorial at http://evomics.org/learning/genomics/satsuma/

Address of the bookmark: http://satsuma.sourceforge.net/

http://compbio.cs.toronto.edu/prism/

Address of the bookmark: http://compbio.cs.toronto.edu/prism/

1. Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
2. Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
3. Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
4. African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
5. European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
6. Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
7. California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
8. Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
9. Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
10. Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
11. GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
12. All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
13. 1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
14. Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
15. Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
16. Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.

Canu is a hierachical assembly pipeline which runs in four steps:

• Detect overlaps in high-noise sequences using MHAP
• Generate corrected sequence consensus
• Trim corrected sequences
• Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

Smart BLAST (https://ncbiinsights.ncbi.nlm.nih.gov/2015/07/29/smartblast/)

Select one or a group of ORFs and BLAST several databases at once, and use the newly developed SmartBLAST to verify protein names. Looking for the traditional results from BLAST? They’re there too.