BOL: Related items

Comparative genomics educational material and papers bookmarks

Jit — Wed, 09 Nov 2016 16:23:30 -0600

Alignment of the porcine genome against seven other mammalian genomes (Supplementary Information) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500 kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60 Myr ago². This rate compares to ~1.9 rearrangements per million years within the primate lineage (Supplementary Table 11). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.

Address of the bookmark: http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.

Shruti Paniwala — Wed, 01 Jun 2022 02:01:13 -0500

Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.

Address of the bookmark: https://github.com/schneebergerlab/syri

Two postdoc positions to study multiscale genome evolution and cephalopod gene regulation (University of Vienna, Austria)

Thu, 17 Dec 2020 11:45:16 -0600

Vienna Biocenter are seeking two postdoctoral researchers to join our team and work on the ERC funded project "METASCALE: Modes of genome evolution during major metazoan transitions". The task of both positions will be to study co-evolutionary trends within animal genomes and their association with the emergence of new gene regulation. Our group employs methods of comparative and regulatory genomics to study the regulatory impact of transitions in animal genome architecture. More recently, we have identified a major genome reorganization in the "smart" coleoid cephalopod molluscs (squid, octopus, cuttlefish) that, together with other genomic changes, potentially comprises a unique path or mode of genome evolution among animals. We are thus interested in quantifying these modes of genome evolution across all available animal genomes and to test whether their shifts are associated with the emergence of novel regulation (e.g., in cephalopods). One of our main model species is the Hawaiian bobtail squid species Euprymna scolopes. The tasks of the two candidates will be complimentary and highly collaborative with one position focusing on comparative genomics analyses across all metazoans and the other position on regulatory genomics in the squid. A solid background in in bioinformatics and comparative genomics is highly desired for the first position, whereas the second position will benefit from experience in molecular and regulatory genomics methods such as HiC, ATAC-seq, RNA-seq or single cell transcriptomics.

The postdocs will join an international group and network of researchers at the University of Vienna studying a diverse range of species and questions in molecular evolution, development, morphology and genomics. Our group is also part of the large evolVienna network of more than 50 evolutionary biology labs in Vienna, across several universities and research institutes. Our Faculty will be relocating to a new campus at the Vienna Biocenter in summer 2021 (https://biologiezentrum.univie.ac.at/en/). Vienna is a vibrant historic European capital with a high QOL. Information about postdoctoral salaries in Austria can be found on this webpage: https://www.fwf.ac.at/en/research-funding/personnel-costs/

Earliest start date will be after July 2021. Initial term of employment is for two years with the possibility of extension. Remote working, at least initially, is a possibility.

Requirements:
- PhD degree or equivalent by the start date
- Publishing record in peer-reviewed journals or evidence thereof
- At least 2 letters of support

Applications including a letter of motivation should be submitted via the Job Center to the University of Vienna (https://personalwesen.univie.ac.at/en/jobs-recruiting/job-center/,
job reference number 11615).

Application deadline: January 15th 2021.
Application link: https://univis.univie.ac.at/ebewerbung

Postdoc in Genomics of Pipefishes and Seahorses at NSF-funded postdoctoral project in Adam Jones' Lab

Thu, 07 Jan 2021 21:22:24 -0600

An NSF-funded postdoctoral position is available in Adam Jones' Lab
at the University of Idaho to study the evolution and development of
the male's brood pouch in syngnathid fishes (seahorses, pipefishes
and seadragons). The project is being conducted in collaboration
with Dr. William Cresko's group at the University of Oregon. The
postdoc will be involved in studies of comparative genomics across
the family Syngnathidae, investigations of brood pouch morphology, and
characterization of the brood pouch microbiome. The position will be
funded for two years, with the possibility of a third year. The postdoc
will be based at the University of Idaho and will interact extensively
with the Cresko Lab at the University of Oregon.

The University of Idaho is in Moscow, a small college town located in
Northern Idaho on the Washington border. Moscow is widely considered to
be a great place to live, and it's known for a pleasant downtown, active
farmer's market, and nearby recreational opportunities. All of Moscow
is within biking or walking distance of the University of Idaho. For
more information about Moscow, see https://visitmoscowid.com/.

The University of Idaho has very strong faculty in evolution and
genomics in multiple departments and interdisciplinary programs. Of
particular note are the Bioinformatics and Computational Biology
Program (BCB: https://www.uidaho.edu/sci/bcb/people/faculty) and
the Institute for Bioinformatics and Evolutionary Studies (IBEST:
https://www.ibest.uidaho.edu/index.php). In addition, the University of
Idaho is only eight miles from Washington State University in Pullman, and
faculty from the two institutions interact and collaborate extensively.

Minimum qualifications include: a Ph.D. in biological sciences,
bioinformatics, or a related discipline; experience conducting research
in genomics or evolutionary biology, as evidenced by publications
in peer-reviewed journals; and evidence of strong written and oral
communication skills. Experience analyzing next-generation sequence
data and familiarity with the genomics of marine fishes are desirable
but not required.

Apply at: https://uidaho.peopleadmin.com/postings/30003

Review of applications will begin January 15, 2021. The start date
is flexible.

The University of Idaho is an equal opportunity/Affirmative Action/equal
access employer.

Informal inquiries are encouraged and can be directed to Adam Jones
(adamjones@uidaho.edu).

"adamjones@uidaho.edu"

Unlocking Evolutionary Secrets: A Dive into Comparative Genomics Methods

LEGE — Tue, 20 May 2025 00:25:09 -0500

Comparative genomics is the art and science of comparing genomes—across species, within species, or even among individuals—to unravel evolutionary relationships, functional elements, and genetic adaptations. As sequencing technologies have advanced and genome databases have expanded, comparative genomics has become a cornerstone of modern biology, shedding light on everything from antibiotic resistance in bacteria to human disease genetics.

In this post, we’ll explore the core methods used in comparative genomics, the questions they help answer, and how they’re shaping our understanding of life.

1. Whole-Genome Alignment
Whole-genome alignment involves mapping the entire genome of one species to another. Tools like MUMmer, MAUVE, and LASTZ perform large-scale sequence alignments to detect conserved regions, rearrangements, insertions, and deletions.

Use Case:
Comparing human and chimpanzee genomes to identify evolutionary conserved sequences (ECS) and regions of divergence.

Key Challenges:
Handling repetitive sequences and genome rearrangements.

Computational complexity in large genomes.

2. Synteny and Collinearity Analysis
Synteny refers to conserved blocks of gene order across species. Tools like MCScanX, SynMap, or CHITRA (for visualizing synteny interactively) detect these blocks to understand chromosomal evolution.

Use Case:
Studying ancient genome duplications in plants.

Investigating chromosomal rearrangements in cancer genomes.

3. Ortholog and Paralog Detection
Orthologs are genes in different species that evolved from a common ancestor, while paralogs are genes duplicated within a genome. Identifying them is crucial for functional annotation and evolutionary studies.

Popular Tools:
OrthoFinder, Orthologous MAtrix (OMA), InParanoid, and EggNOG.

Use Case:
Functional prediction of uncharacterized genes based on orthologs in model organisms.

Tracing gene family evolution.

4. Phylogenomic Analysis
Phylogenomic methods combine phylogenetics and genomics to infer evolutionary trees based on genome-wide data. These methods can handle dozens to hundreds of genomes, using concatenated alignments or gene trees.

Tools:
RAxML, IQ-TREE, ASTRAL, Phylip, BEAST.

Use Case:
Resolving the evolutionary relationships between microbial species.

Studying speciation events.

5. Pan-Genome Analysis
The pan-genome consists of the core genome (shared by all strains) and the accessory genome (strain-specific genes). This is especially popular in microbial genomics.

Tools:
Roary, Panaroo, BPGA, PGAP.

Use Case:
Understanding virulence factor diversity in E. coli.

Designing broad-spectrum vaccines.

6. Comparative Transcriptomics
Comparing transcriptomes across species or conditions reveals conserved and unique expression patterns. RNA-seq data can be mapped to reference genomes to identify orthologous expression profiles.

Use Case:
Comparing stress response in extremophiles and model species.

Studying conserved regulatory networks.

7. Functional Element Comparison
Beyond genes, comparative genomics also targets non-coding regions—enhancers, promoters, miRNAs. Conservation across species often implies functional importance.

Tools:
PhastCons, GERP, phyloP (based on multiple alignments).

Use Case:
Detecting conserved non-coding elements in vertebrates.

Studying regulatory divergence in human evolution.

8. Horizontal Gene Transfer (HGT) Detection
In microbes, genes often jump across species boundaries. Comparative genomics can detect HGT by identifying genes that defy the expected phylogenetic pattern.

Tools:
HGTector, DarkHorse, AlienHunter, SIGI-HMM.

Use Case:
Tracing antibiotic resistance genes.

Exploring microbial adaptability in extreme environments.

Final Thoughts
Comparative genomics is a powerful lens to observe the diversity and unity of life. With a broad toolkit—from aligners to orthology pipelines, phylogenetic engines to visualization tools—it allows scientists to ask big questions: How did genomes evolve? What makes species unique? Where do new genes come from?

Whether you're studying extremophiles, building better crops, or exploring human ancestry, comparative genomics offers the methods to connect the dots across the tree of life.

G-compass: a comparative genome browser

Jit — Thu, 12 Apr 2018 10:00:27 -0500

G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

postdoctoral fellow for a large-scale microbial comparative genomics !

Thu, 29 Apr 2021 08:44:53 -0500

Asaf Levy hiring a postdoctoral fellow for a large-scale microbial comparative genomics project at the Hebrew University of Jerusalem (Israel).
The project is a continuation of Levy Asaf et al. Nature Genetics 2018 paper.
Requirements:
1.Experience with programming in at least one programming language, preferably Python.
2.A PhD in bioinformatics/computational biology
3.At least one first authorship publication in a good journal, preferably more.
4.Good communication skills in English
5.Ability to enter and study in Israel (not applicable for Pakistani people, for example).
6.Ability to work in a team.
Please send CV to alevy@mail.huji.ac.il

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/