BOL: Related items

TMRCA Calculator

BioStar — Wed, 03 Feb 2021 05:07:30 -0600

This program calculates the probability that two people have a certain number of generations between them, based on the standard infinite alleles formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.

https://clandonaldusa.org/index.php/tmrca-calculator

Address of the bookmark: https://clandonaldusa.org/index.php/tmrca-calculator

Chromosome breakpoint - a breakup to remember

BioStar — Tue, 07 Mar 2023 13:31:54 -0600

Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be induced by environmental factors such as radiation, chemicals, or viruses. The rearrangement of genetic material resulting from a chromosome breakpoint can have important consequences, including the development of genetic diseases, chromosomal abnormalities, or cancer.

Chromosome breakpoints can occur in two ways: interstitial or terminal. Interstitial breakpoints occur within the chromosome, while terminal breakpoints occur at the end of the chromosome. Terminal breakpoints can lead to the loss of genetic material, whereas interstitial breakpoints can result in the duplication or deletion of genetic material.

Chromosome breakpoints can be detected using a variety of techniques, including cytogenetic analysis, fluorescence in situ hybridization (FISH), and molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing (NGS). These techniques can also help identify the exact location of the breakpoint and the nature of the rearrangement, such as translocations, inversions, deletions, or duplications.

Translocations are one of the most common types of chromosome rearrangements caused by breakpoints. In a translocation, genetic material is exchanged between two different chromosomes, resulting in a balanced or unbalanced distribution of genetic material. Unbalanced translocations can cause genetic diseases or developmental abnormalities, while balanced translocations can be inherited without any apparent phenotypic effects.

Inversions occur when a chromosome segment is inverted, resulting in a change in the order of genetic material. Inversions can be pericentric, involving the centromere, or paracentric, not involving the centromere. Inversions can cause genetic diseases or phenotypic effects if they disrupt the function of essential genes or regulatory elements.

Deletions and duplications are caused by interstitial breakpoints that result in the loss or gain of genetic material. Deletions can cause genetic diseases or developmental abnormalities if they involve essential genes or regulatory elements. Duplications can also have phenotypic effects, depending on the location and size of the duplicated segment.

Chromosome breakpoints can also be involved in the formation of complex chromosomal rearrangements, such as ring chromosomes or dicentric chromosomes. These complex rearrangements can have important clinical implications, as they can cause genetic diseases or cancer.

In conclusion, chromosome breakpoints are important genetic events that can lead to the rearrangement of genetic material and have important clinical implications. The detection and characterization of chromosome breakpoints using cytogenetic, molecular, and genomic methods are essential for the diagnosis, prognosis, and treatment of genetic diseases and cancer. Further research is needed to understand the molecular mechanisms underlying chromosome breakage and to develop new therapies targeting these events.

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.

Phylogenetics

Fri, 23 Aug 2013 03:53:43 -0500

006 - Phylogenetics Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data. A specific type of phylogenetic tree, the cladogram, is also covered. Intro Music Atribution Title: I4dsong_loop_main.wav Artist: CosmicD Link to sound: http://www.freesound.org/people/CosmicD/sounds/72556/ Creative Commons Atribution License

Mike Ritchie Lab

Wed, 02 Oct 2013 15:25:45 -0500

Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new statistical methods with a focus on the detection of gene-gene interactions associated with human disease.

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

GPS DNA tracking - University of Sheffield

Sat, 10 May 2014 04:33:28 -0500

University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

Post-Doc Positions at the Institute of Evolution, University of Haifa, Haifa, Israel

Thu, 04 Sep 2014 03:59:38 -0500

We are looking for independent, motivated, diligent, laborious, dedicated Bioinformaticians as post-doctorate fellows for a project aimed at revealing the mechanisms of cancer-resistance and anti-cancer activity of the hypoxia-tolerant subterranean, blind mole-rat, Spalax along its underground evolutionary adaptations. Our project has captured the interest of the scientific community and we have ample financial support for the studies. Generous fellowships ($30K to $40K according to qualifications and performance) are available, immediately, for Post-Docs experts in bioinformatics with a background of good understanding biological questions. That is that can independently handle raw output data of RNA-seq / miR seq/ Genomic, analyze it and can interpret intelligently the relevant biological background. Outstanding candidates for PhD experienced in Bioinformatics will also be considered. Familiarity with cancer research is an advantage. Experience of writing manuscripts for publication and a publication record in relevant journals are expected. English skills both oral and written are required. American, Western-European or Israeli education is a significant benefit.

Our present objectives is to identify and isolate the substances secreted by Spalax cells, resolve with which components they interact that are active only on cancer cells, in order to unravel the biological mechanisms and pathways that evolved in Spalax cell machinery and ultimately lead to the death of cancer-cells. The study could attest to be a breakthrough in cancer research, using the long lived, hypoxia- and cancer-tolerant Spalax as a significant biological resource for biomedical research that hopefully could open new horizons in treatment and prevention of cancer in humans.

Contact: The applications should be submitted, together with extended CV and bibliography, summary of past accomplishments, and contact information of 3 referees, to Prof of Research Aaron Avivi (aaron@research.haifa.ac.il) AND Dr. Imad Shams (imadshams@gmail.com). (http://bit.ly/1lywShk) aaron@research.haifa.ac.il

More at http://evolution.haifa.ac.il/index.php/29-people/personal-websites/77-personal-site-avivi

Manolis Kellis Lab

Sun, 31 Jan 2016 20:51:06 -0600

A major focus of our lab is understanding the effects of genetic variation on molecular phenotypes and human disease. We develop methods for integrating diverse functional genomic datasets of transcription, chromatin modifications, regulator binding, and their changes across multiple conditions to interpret genetic associations, identify causal variants, and predict the effects of genetic perturbations.

More at http://compbio.mit.edu

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full