BOL: Related items

Mitochondrial genome assembly tools !

Abhi — Wed, 06 Sep 2023 00:37:18 -0500

Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS). The mitochondrial genome is relatively small compared to the nuclear genome, making it an ideal target for assembly. Here are some commonly used mitochondrial genome assembly tools:

MitoFinder: Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

MITObim: MITObim is a tool specifically developed for the iterative assembly of mitochondrial genomes. It starts with a reference mitogenome and iteratively refines the assembly using the read data.

MITOS: MITOS is a web-based platform that provides a pipeline for annotating mitochondrial genomes. It integrates multiple software tools for assembly, annotation, and visualization of mitogenomes.

MIRA: MIRA (Mimicking Intelligent Read Assembly) is a versatile genome assembly tool that can be used for mitochondrial genome assembly. It supports various sequencing technologies and allows for reference-based or de novo assembly.

NOVOPlasty: NOVOPlasty is a user-friendly tool designed for de novo assembly of organelle genomes, including mitochondria. It utilizes a seed-and-extend algorithm and is suitable for both short-read and long-read data.

MITOS2: MITOS2 is an updated version of the MITOS pipeline, which automates the annotation of mitochondrial genomes. It provides improved accuracy and additional features for mitochondrial genome analysis.

GetOrganelle: While primarily designed for chloroplast genome assembly, GetOrganelle can also be used for mitochondrial genome assembly. It is particularly useful for dealing with high-throughput sequencing data.

SPAdes: SPAdes (St. Petersburg genome assembler) is a versatile genome assembly tool that can be employed for mitochondrial genome assembly, especially when dealing with complex datasets that may contain nuclear mitochondrial DNA sequences (numts).

IDBA-UD: IDBA-UD (Iterative De Bruijn Graph De Novo Assembler) is another de novo assembly tool that can be used for mitochondrial genome assembly, especially in cases with relatively low coverage.

Velvet: Velvet is a de novo assembly tool that can be applied to mitochondrial genome assembly, especially when working with short-read data.

When selecting a mitochondrial genome assembly tool, it's important to consider the specific characteristics of your sequencing data, such as read length and coverage, as well as the complexity of the mitochondrial genome. Additionally, some tools are better suited for specific organisms or research objectives, so choosing the right tool will depend on your particular project requirements.

JNU Neuroscience/Systems Biology/Mathematical modeling JRF Vacancies

Fri, 26 Dec 2014 11:22:20 -0600

School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067

Recruitment for Project

Applications were invited from the citizens of India for filling up the following temporary position for the CSIR sponsored Fellowship in the School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067. This position is temporary for a period of two and half years or tenable only for the duration of the project. The requisite qualifications & experience are given below.

Project Title : "Understanding Complex dynamics and Information processing in Brain Networks"
Funding Agency : CSIR

Principal Investigator : Dr. R.K. Brojen Singh

Position : Junior Research Fellow(One post)

Salary : As per CSIR rules and guidelines for JRF.

Qualifications & Experience : M.Sc. in Physics/Mathematics/Biology/B.Tech. In Eng. Physics/Comp. Sc. and desirable CSIR-UGC NET Qualified. Candidates should also have at least one years research experience after M. Sc./B.Tech. in works related to Neuroscience/Mathematical modeling.

Candidates possessing requisite qualifications may apply either on plain paper stating the project title along with CV and send to the following address or send as email attachment (pdf or word format) so as to reach on or before 8 January, 2014.

Dr. R.K. Brojen Singh
School of Computational and Integrative Sciences
Jawharlal Nehru University
New Delhi 110067
Email: brojen@jnu.ac.in, brojen@mail.jnu.ac.in

When Chromosomes Shift: Understanding Chromosome Rearrangement and Human Disease

BioStar — Fri, 11 Apr 2025 01:07:17 -0500

In the vast and complex world of genetics, our chromosomes are like carefully arranged bookshelves — each holding critical information that defines who we are. But what happens when those books are shuffled, inverted, or swapped? The answer lies in a phenomenon known as chromosome rearrangement, a powerful force behind many human diseases, from developmental disorders to cancer.

What Are Chromosome Rearrangements?

Chromosome rearrangements are structural changes that alter the normal configuration of chromosomes. These changes can involve large segments of DNA — from thousands to millions of base pairs — and can occur spontaneously, be inherited, or result from exposure to mutagens (like radiation or chemicals).

Common Types of Rearrangements:

Deletions – Loss of a chromosome segment
Duplications – Repetition of a segment
Inversions – A segment breaks off, flips, and reattaches
Translocations – Segments exchange places between non-homologous chromosomes
Insertions – A segment is inserted into another part of the genome

These changes can disrupt genes directly or affect gene regulation, leading to disease.

How Do Chromosome Rearrangements Cause Disease?

The impact of a rearrangement depends on which genes are involved, how much DNA is affected, and when the rearrangement occurs (in development vs. adulthood). Here are some key mechanisms:

Gene disruption: Breaking a gene can lead to loss of function or the creation of a non-functional protein.
Gene fusion: Joining parts of two genes may form a novel hybrid gene with new functions (common in cancer).
Dosage effects: Extra or missing gene copies can disturb the balance of gene expression.
Position effects: Moving a gene to a new regulatory environment may silence or over-activate it.

Chromosome Rearrangements in Human Disease

1. Developmental Disorders

Cri-du-chat syndrome: Caused by a deletion on chromosome 5p. Affected infants often have a high-pitched cry and intellectual disability.
Williams syndrome: Results from a microdeletion on chromosome 7q, affecting genes related to cardiovascular and cognitive function.

2. Cancer

Cancer is perhaps the most striking example of disease caused by chromosome rearrangements.

Chronic Myeloid Leukemia (CML): Caused by a translocation between chromosomes 9 and 22, forming the Philadelphia chromosome. This creates the BCR-ABL fusion gene, which drives uncontrolled cell growth.
Burkitt lymphoma: Involves translocation of the MYC gene, leading to excessive cell division.
Ewing sarcoma: A fusion of EWSR1 and FLI1 genes through translocation promotes tumor development.

3. Infertility and Miscarriages

Balanced rearrangements (like inversions or translocations) in carriers may not cause disease directly but can result in:

Recurrent miscarriages
Infertility
Birth defects in offspring

Detecting Rearrangements

Thanks to modern genomics, chromosome rearrangements can now be detected with high precision using:

Karyotyping – Classic method for detecting large rearrangements
FISH (Fluorescence In Situ Hybridization) – Uses fluorescent probes to target specific DNA sequences
Array CGH (Comparative Genomic Hybridization) – Detects copy number changes across the genome
Whole Genome Sequencing (WGS) – Identifies even small or complex rearrangements at base-pair resolution

Looking Forward: The Future of Chromosome Medicine

Understanding chromosome rearrangements is now central to:

Personalized medicine
Genetic counseling
Targeted therapies, especially in cancer (e.g., tyrosine kinase inhibitors for BCR-ABL fusion)

With the rise of long-read sequencing and single-cell genomics, even previously “invisible” rearrangements are being uncovered, offering new insights into both rare diseases and common conditions.

Final Thoughts

Chromosome rearrangements remind us that genetics isn't just about which genes we have — but where they are, how they're arranged, and when they're active. As our tools grow sharper, so does our ability to diagnose, understand, and treat diseases rooted in genomic architecture.

In a way, the genome is like a book not just defined by its words, but also by how the chapters are ordered. Rearranging them can create a new story — sometimes harmful, sometimes insightful — and understanding these changes is key to writing a healthier future.

Zhang Lab

Sun, 28 Dec 2014 12:43:08 -0600

We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.

More at http://bioinfo.vanderbilt.edu/zhanglab/

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

Illumina Smartphone Chip !!!

Robert M Willioms — Tue, 30 Dec 2014 23:19:54 -0600

Illumina, the company that claims it brought human genome sequencing down to $1000 prices, has now turned its attention to a consumer product - a chip that you can plug into your smartphone and have it read your genetic information.

The biggest challenge ahead of Illumina is simplifying the process of genetic sequencing. Currently, Illumina’s DNA sequencers are gigantic machines that use techinques like colorimetry to work, but while the core technology is computational, it takes some 30 steps to extract genetic data and run it through. This process will likely have to be hugely simplified on mobile devices, given the fact that some studies require extracting 10 mililiters of blood. Illumina researchers are also working on finding the optimal technology for this on-chip DNA sequencing - be it electrical, optical, or other.

Illumina is one of the most prominent names in genetics, often said to be the Intel of genetic sequencing, as just like Intel it provides the algorithms, the processing brain that runs a DNA reading task.

In other recent smartphone-related biotech news, drug company Pfizer launched its REMOTE project, a new type of clinical trial that does not require going to a hospital for checks - targeted at patients with overactive bladder problems, the FDA-approved REMOTE project allowed to gather data from patients from over 10 states remotely, via mobile devices.

This is indeed the Illumina answer to Apple's Health app, HealthBook, Google HealthFit.

Sorghum genome Sequenced!!

Jit — Sun, 01 Sep 2013 19:46:18 -0500

Sorghum, a staple food for 500 million resource-poor people in marginal environments and a model for other important crops, sorghum holds vital genetic resources as humanity confronts the nexus of food crisis and climate change. The recent research provides an unmatched resource to respond to these challenges by identifying a large high-quality SNP and indel data set in diverse sorghum genotypes.

In addition to providing a broad sample of the diversity in S. bicolor, the genotypes included in this study are known to display agronomically important traits including stay-green drought resistance, insect resistance, grain size and grain quality.

Find more at http://www.nature.com/ncomms/2013/130827/ncomms3320/full/ncomms3320.html

WALK-IN-INTERVIEW for the post of JRF and Project Assistant @ CIFT

Tue, 20 Jan 2015 23:03:20 -0600

Eligible candidates are invited to attend a walk-in-Interview with all relevant documents for the following positions of Project Fellows (on contractual basis) to work in the Project “ Genetic Diversity of Clostridium botulinum in seafood and Development of Lateral Flow Immuno Assay (LFIA) for toxinotyping funded by Department of Biotechnology. The duration of the project is 3 years / co-terminus with the scheme.

Jr. Research Fellow – 2 posts

Fellowship : Rs. 25000/- + 20% HRA pm for Ist & 2nd year and Rs.28000/- + HRA on 3rd year

Qualification : Ist class Masters Degree in Microbiology/Fishery Microbiology/Bio-technology.

Desirable :

1. CSIR/UGC NET/JRF qualified

2. Excellent analytical skills and computer documentation

3. Prior experience in handling microbial cultures and molecular techniques

Project Assistant – 1 post

Fellowship : Rs.8000/- p.m (consolidated)

Qualification: Masters degree in Microbiology/Biotechnology with skill in Bioinformatics

Desirable: Excellent analytical skills in Bioinformatics and computer documentation

Terms & Conditions:

Registration will begin at 8.30 a.m and will close at 11.00 am
Age limit (as on 29.1.2015): Below 35 years for men and 40 years for women.
Age relaxation of 3 year for OBC candidates and 5 years for SC/ST candidates is permissible.
Candidates are required to submit self-attested copies of all the Certificates in support of their claims regarding age, educational qualifications, scheduled caste/scheduled tribe/OBC etc. The original certificates shall be produced for verification before the interview.
Candidates should bring detailed bio-data (in the enclosed format) affixing a recent passport size photograph.
The selected candidate will be recruited on contract basis under ICAR norms. The post is purely temporary and is co-terminus with the project.
The candidates attending the interview should ensure that they fulfil all the eligibility conditions. No correspondence will be entertained from the candidates for selection/test/appointment.
No TA/DA will be paid to attend the interview.
Canvassing in any form will render the candidate disqualified for the post.
The Director’s decision will be final and binding in all aspects regarding the selection to the post.

Venue: CIFT, Matsyapuri.P.O, Cochin Date of interview: 29.01.2015 Time: 10.00 am

http://www.cift.res.in/uploads/userfiles/file/file/srf%20appn.doc

Genetics, epigenetics and disease

Fri, 27 Sep 2013 11:32:55 -0500

Royal Society GlaxoSmithKline Prize Lecture given by Professor Adrian Bird CBE FMedSci FRS on Tuesday 22 January 2013. Adrian Bird CBE FMedSci FRS is the Buchanan Chair of Genetics at the University of Edinburgh. The human genome sequence has been available for more than a decade, but its significance is still not fully understood. While most human genes have been identified, there is much to learn about the DNA signals that control them. This lecture described an unusually short DNA sequence, just two base pairs long, CG, which occurs in several chemically different forms. Defects in signalling by CG are implicated in disease. For example, the autism spectrum disorder Rett syndrome is caused by loss of a protein that reads methylated CG and affects the activity of genes. The Royal Society GlaxoSmithKline Prize Lecture is awarded for original contributions to medical and veterinary sciences published within ten years from the date of the award.

WALK-IN-INTERVIEW FOR PROJECT ASSISTANT @ BHARATHIDASAN UNIVERSITY

Mon, 12 Jan 2015 21:54:10 -0600

BHARATHIDASAN UNIVERSITY
DEPARTMENT OF BIOINFORMATICS, SCHOOL OF LIFE SCIENCES, TIRUCHIRAPPALLI – 620024

Project title: “Genome-scale metabolic modeling and simulation of rumen methanogens An in silico attempt to methane attenuation”

Funding Agency: University Grants Commission, New Delhi

Tenure of the project: Two years or till the end of the project period.

Position: Project Assistant (1 no.)

Essential qualification: First class M.Sc. in Bioinformatics/Microbiology/ Biotechnology and other related discipline.

Desirable qualification: Experience in an area relevant (Molecular Systems Engineering) to the project.

Fellowship: Rs. 5000 per month as per the UGC norms.

Upper age limit: 28 years

Date of Venue of interview: 22.01.2015, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli -620 024, Tamil Nadu

The above post is purely temporary and will be terminated with three month notice.

The Terms and the condition of the appointment shall be governed according to UGC, Govt. of India. The eligible candidates will bring their original certificates and documents at the time of interview. No TA/DA will be paid for attending the interview.

Dr. P. CHELLAPANDI
UGC-Research Awardee,
Department of Bioinformatics,
School of Life Sciences,
Bharathidasan University,
Tiruchirappalli -620 024, Tamil Nadu

Advertisement: www.bdu.ac.in/adv/PA_UGC_Bioinformatics.pdf