BOL: Related items

Assistant Professor (Bio-Informatics) at Health and Family Welfare Department (Medical Education) in Raipur

Wed, 07 May 2014 00:08:38 -0500

Advertisement No.05/2014/ Exam/Dated 17/04/2014

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

NearHGT

Jit — Wed, 22 Jun 2016 05:41:57 -0500

Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive.

We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set.

When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Availability: The method is publicly available athttp://research.haifa.ac.il/~ssagi/software/nearHGT.zip

Address of the bookmark: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004408

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)

Abhimanyu Singh — Thu, 29 Dec 2016 03:26:45 -0600

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:

Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
Open Source: Prodigal source code is freely available under the General Public License.

Download the latest version of Prodigal at the Prodigal github page.
or
Browse the wiki documenation.

Address of the bookmark: http://prodigal.ornl.gov/

Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events

Jit — Sun, 07 Jan 2018 19:11:18 -0600

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs).

An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/alien-hunter

GenomeThreader: Gene Prediction Software

Neel — Wed, 03 Oct 2018 15:34:08 -0500

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation.

Address of the bookmark: http://genomethreader.org/

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

Abhi — Mon, 10 Jan 2022 06:32:22 -0600

This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detection of HGTs, along with retrieval of information about those OGs that are monophyletic with organisms from cellular domains of life.

https://www.readcube.com/articles/10.3390%2Fv9040072

Address of the bookmark: https://pubmed.ncbi.nlm.nih.gov/28387730/

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence

Poonam Mahapatra — Sat, 02 Jun 2018 07:38:33 -0500

GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

Address of the bookmark: https://sourceforge.net/projects/glean-gene/

GeneOverlap: An R package to test and visualize gene overlaps

Jit — Thu, 27 Dec 2018 19:45:52 -0600

Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf

ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes

Jit — Tue, 14 Jul 2020 06:42:10 -0500

ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in prokaryotes.

https://www.mdpi.com/2073-4425/11/7/756/htm

https://shadowcaster.readthedocs.io/en/latest/

https://github.com/dani2s/ShadowCaster_testData

Address of the bookmark: https://github.com/dani2s/ShadowCaster