BOL: Related items

Genomicus: genome browser that enables users to navigate in genomes in several dimensions

Jit — Mon, 28 Feb 2022 23:27:37 -0600

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.

Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)


Number of extant species	200
Number of extant genes	4303993
Number of ancestral species	196
Number of ancestral genes	4624213
Number of ancestral synteny blocks	83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

Genetic basis of tail-loss evolution

LEGE — Tue, 04 Mar 2025 12:12:36 -0600

The paper "On the genetic basis of tail-loss evolution in humans and apes (https://www.nature.com/articles/s41586-024-07095-8)", published in Nature, investigates the genetic mechanisms that led to the loss of tails in humans and apes. The study suggests that a specific genetic mutation, involving the insertion of an Alu element (a type of transposable DNA sequence), played a critical role in the evolutionary transition from tailed primates to tailless hominoids.

Key Findings of the Study:

Alu Insertion and Tail Loss:
The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.
Gene Disruption Mechanism:
The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.
Functional Evidence from Model Organisms:
To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.
Evolutionary Implications:
The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.
Relevance to Human Evolution:
Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

BioStar — Thu, 13 Aug 2020 09:57:24 -0500

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/#

STELLAR: fast and exact local alignments

Neel — Wed, 29 Aug 2018 16:00:46 -0500

STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar.

Address of the bookmark: http://www.seqan.de/apps/stellar/

BINC examination 2015 !!!

Jitendra Narayan — Mon, 29 Dec 2014 12:23:37 -0600

Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination in 2015. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.Registration for BINC examination 2015 will open soon.

Pondicherry University Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, Pune University, Pune; Anna University, Chennai; Calcatta University (WBUT) Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; University of Kerala, Thiruvananthapuram; Jawaharlal Nehru University, New Delhi and Assam Agricultural University, Guwahati.

In the BINC 2013 examination,17 candidates were certified. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://210.212.230.224:9999/BINC/

BCIL Bioinformatics BITP Application !!

Pranjali Yadav — Fri, 17 Apr 2015 04:34:56 -0500

BCIL Bioinformatics BITP Application Form 2015 logoGrab latest Information! Biotech Consortium India Limited has announced a notification for offering admission in Biotech Industrial Training Program. The organization has invited online application from 7th April 2015 BCIL Admission 2015. BCIL has conducted an entrance exam which is scheduled on 20th June 2015. Candidates those who are looking for this program just go for it and don’t miss this opportunity.

To apply for Biotech Industrial Training Programme the candidates should have 50% marks in B.Tech/BE/M.Tech Degree in Bio technology, bio process technology and other related disciplines form any recognized institution. The organization has decided application fee of Rs.500/- for all candidates and that should be paid through demand draft. Applicants who satisfy the organization requirement, they can take their steps forward.

Candidates should submit the online application before 10th May 2015. After registering the online application you need to take the hard copy of it and send through post. Print out of this application should be reached before 15th May 2015. All the latest updates like selection process, exam syllabus and other related information are updated soon at the main URL of the department and aspirants should keep in touch with this site. Further details of BCIL Bioinformatics BITP Application Form 2015 are explained below.

Organization: Biotech Consortium India Limited

Website URL: www.bcil.nic.in

Location: New Delhi

Course Name: Biotech Industrial Training Program

Exam Name: BCIL Entrance Exam

Educational Details: Applicants should complete their B.Tech/M.Tech/BE programs in Neuro- Science, Agricultural, Bio technology, bio process technology and other related disciplines having 50% aggregate from any authorized university.

Application Fee: For all candidates application fee is Rs.500/- and it will be paid through Demand Draft drawn in favour of BCIL, New Delhi.

How to Apply: Candidates who are willing to apply for this program they can apply through online mode. Then send the hard copy of registered application form to through post.

Important Dates

Opening Date of Submission Online Application Form: 7h April 2015

Closing Date of Submission of Online Application Form: 10th May 2015

Last Date of Receipt of Application Form: 15th May 2015

Exam Date: 20th June 2015

More at http://bcil.nic.in/default.htm

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:14:14 -0500

BINC sample question paper round TWO.

Perl One liner basics !!

Abhimanyu Singh — Sun, 24 May 2015 09:28:33 -0500

Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:

$ perl -e 'print "Hello, World!\n"'
Hello, World!

It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.

I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?

$ perl -e 'print "$^O\n"'
linux

It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:

$ perl -E 'say "$^O"'
linux

Pretty handy! say is a nifty feature that you'll use again and again.

Rosalind Problem Solution with Perl

Jit — Tue, 09 Jun 2015 23:35:18 -0500

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...