Address of the bookmark: https://chunlab.wordpress.com/tetra-nucleotide-analysis/

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

How to use TAREAN:

• Install a local instance of the pipeline using its source code available from bitbucket repository.
• Use  public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

Address of the bookmark: https://github.com/lh3/ropebwt2

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can make specific classifications, exploiting point mutations to distinguish close taxa. AA-based classifiers have higher sensitivity in detecting homology between query and reference sequences, leverageing higher conservation of AA sequences. Metabuli combines the information of both sequence types using a novel k-mer structure, metamer, to enable both specific and sensitive characterization of metagenomic samples. In addition, it can classify reads against a database of any size as long as it fits in the hard disk.

Address of the bookmark: https://github.com/steineggerlab/Metabuli

There are Neanderthal bones. Denisovan remains. Fossils from ancient relatives of our species. Each specimen gives us another piece of the story of how Homo sapiens came to be.

But now imagine that one of the most important characters in that story has left behind no fossil, no skull, no bone, and no genome.

Nothing that a paleontologist could put behind glass.

And yet, somehow, that ancient population is still speaking.

It is speaking through us.

A fascinating new study published in Science (https://www.science.org/doi/10.1126/science.aef8874?) introduces a computational method called TRACE, which allows scientists to search modern human genomes for genetic traces of ancient populations that have never been directly identified.

For years, scientists have known that our ancestors interacted with Neanderthals and Denisovans. Their DNA still survives in modern human populations. But these may not have been the only ancient humans who crossed paths with our ancestors.

Using TRACE, researchers found evidence of an unknown archaic population that contributed DNA to the ancestors of modern humans before humans spread beyond Africa.

Even more surprisingly, they found evidence of a much older lineage—possibly around 1.8 million years old—whose genetic legacy may have reached some modern humans indirectly through Denisovans.

The extraordinary part is that researchers did not need DNA from these mysterious populations to detect them. Instead, they studied the ancestry of modern genomes and looked for genetic patterns that revealed unusually ancient branches of our family history.

It is almost like finding the footprints of someone who disappeared thousands of years ago—without ever finding the person themselves.

These discoveries suggest that human evolution was far more complicated than a simple family tree. Ancient human populations repeatedly separated, migrated, met and exchanged genes. Some eventually disappeared, but pieces of their genetic legacy survived.

And that means our DNA is more than a biological instruction manual.

It is also an archive of human history.

Some of the people recorded in that archive may never have a name or a fossil. But thanks to methods like TRACE, their genetic echoes are finally becoming visible.

The next big discovery about our ancient past may not come from a fossil in the ground.

It may already be inside us.

Reference: Zhang et al., “Recovering signatures of archaic hominin introgression using ancestral recombination graphs,” Science (2026), DOI: 10.1126/science.aef8874. Detail paper @ https://www.science.org/doi/10.1126/science.aef8874?

The TRACE repository (https://github.com/YulinZhang9806/trace) contains the Python package and command-line tools used to infer archaic admixture tracts from ancestral recombination graphs.

Walk- in- Test cum Interview (based on test) for the selection of Research Associate

under the scheme “Distributed Information Sub Centre –DISC” & Research Assistant under scheme “Phytophthora, Fusarium and Ralstonia diseases of Horticultural and Field Crops” will be held at this Institute as per details indicated below.

WALK -IN- TEST CUM INTERVIEW

Name of the post : Research Associate

Date of Interview : 21-05-2014 at 10.00 AM

No. of posts : One

Qualifications : a)Essential

Ph.D Degree in Bioinformatics OR : Masters degree in Bioinformatics with a minimum of
60% marks or equivalent OGPA with at least two years research experience as evidenced from fellowship/ associateship/training/published papers etc.

b)Desirable: Experience in NGS data analysis.

Emoluments : Rs. 23,000/- per month + HRA (Masters Degree Holders)

Rs. 24,000/- per month + HRA (Ph.D Degree Holders)

Upper age limit : 40 years for Men & 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)

Duration of Project : Till 31-03-2017.

Title of Assigment : Research Assistant (on contract basis)

No. of vacancy : One

Qualification : Essential : Post Graduation in Bioinformatics and Minimum one year experience in NGS data analysis

Desirable : Experience in Perl/Python/R

Remuneration : Rs. 20,000/- per month (consolidated)

Scope of work :

1. Analysis of different file formats and their conversions.

2. Assessing the quality of data and filtering of raw reads.
3. Assembling the raw reads-de novo as well as reference mapping.
4. Compression of aligned reads using Jam tools
5. RNA-seq. Analysis
6. Differential expression testing involving Normalization, Statistical testing, heat map generation & hierarchical clustering
7. Annotating the assembled genome and geneet testing and their validation
8. Metabolic pathway analysis
9. Comparative genomics
10. Setting up of genome browsers.

Period of Assigment : Initially for six months.

Date & Venue of Interview : 21-05-2014 at IISR, Kozhikode at 10.00 AM

More at http://www.spices.res.in/pdf/disc-advtmnt.pdf

About JNIAS
Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D. Swaminadhan Research Foundation (DSRF), Hyderabad as a Research and Educational Institution with a view to contribute in developing advanced technologies and build „core competence‟ in specific areas. The activities of JNIAS involves: Education, Research Training and Innovations in the fields of Sciences, Technologies, Humanities and Social Sciences. It aims to blossom into an Advanced Institute of education and research with a reservoir of expertise and experience in the relevant fields and the necessary capability to harness multi-disciplinary research and studies. JNIAS has been recognized as an Advanced Research Institute by Jawaharlal Nehru Technological University Hyderabad (JNTUH), Hyderabad and Jawaharlal Nehru Technological University Anantapur (JNTUA), for offering Ph.D., P.G M.Phil, P.G Diploma and Training Programmes in Sciences and Engineering & Technology.

Jawaharlal Nehru Architecture and Fine Arts University (JNAFAU) Hyderabad also recognized JNIAS for offering UG, PG degree in Architecture.

Projects & Facilities

JNIAS offers wide range of projects:

Biotechnology area:

Molecular Biology
Microbiology
Nanotechnology
Bioinformatics (Schrodinger Software)
In Silico studies & Drug Designing
Sequence analysis
Protein structure function studies

Registration
Tuition Fees: Interested students need to pay the following tuition fees:
1. Six Month’s Project: Rs. 20,000/-
2. Four Month’s Project: Rs. 15,000/-
3. Three Month’s Project: Rs. 10,000/-
4. One Month - Hands on Training : Rs. 8,000/-

For enquires call:
91-7893203414 (Biotechnology), 91-9949582263 (Environmental Sciences) 91-8977369305 (Computer Science)

Interested student may download the application from the website (www.jnias.in) and send the hard copy of the completed application forms and Curriculum Vitae along with the Demand Draft drawn on any nationalized Banks in favor of “The Registrar, JNIAS, Secunderabad”. Application forms can be sent through email to academicprojects@jnias.in

Address
Jawaharlal Nehru Institute of Advanced Studies (JNIAS)
6th Floor, Buddha Bhavan, M.G Road,
Secunderabad - 500 003
Andhra Pradesh, India
Tele/Fax: 040- 27541551; 27541553
Mobile: 08885541554
Web site: www.jnias.in

Brochure : https://drive.google.com/file/d/0B3zPwhgA-u-nU0dyMFd2OWcxNUpSTWNYc0xDSGs5UDI4UDNB/view?usp=sharing

Email: admin@niab.org.in Telephones: +91 40 2304 9403 Telefax: +91 40 2304 2740
Advertisement No: 5/2014

About NIAB National Institute of Animal Biotechnology (NIAB), Hyderabad, an autonomous institute under the aegis of Department of Biotechnology, Government of India, is aimed to harness novel and emerging biotechnologies and create knowledge in the cutting edge areas for improving animal health and productivity.

Applications are invited for the following temporary research positions to work in ongoing DBTBBSRC sponsored research project entitled “Transcriptome Analysis in Indian buffalo and the Genetics of Innate Immunity” at the National Institute of Animal Biotechnology, Hyderabad.

(A) Project Scientist – Level B (One Position)

Emoluments: Rs. 15600 + GP Rs. 5400 + 30 % HRA p.m. (Total emoluments will be Rs. 49,770/-p.m. for the duration of the project)

Essential Qualification: Candidates having M.V.Sc. in Veterinary Microbiology / Veterinary Pathology / Veterinary Public Health / Ph.D. degree in Life Sciences, Biotechnology, Molecular Biology or any other related field from the recognized university are eligible to apply.

The candidate should have a good academic record and research experience as evidenced from published in standard referred journals / patents.

Desirable: Candidates having research experience in the area of tissue culture, genomics, Transcriptomics and Advanced Molecular Biology will be given preference.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

(B) Research Associate in Bioinformatics (One position)

Fellowship: Rs. 22,000 + 30 % HRA

Essential Qualification: Candidates having Ph.D. degree or M.Tech. with three years of
experience in Bioinformatics, Computational Biology, Biotechnology, Life Sciences or any other related field are eligible to apply.

Desirable: Candidate having research experience in the area of next generation sequencing (NGS) data analysis, Genome wide association studies, Genomic selection, advance genomic data analysis etc., will be given preference. The candidate should have a good academic record and research experience as evidenced from published papers in standard journals / patents.

Age Limit: Not exceeding 30 years as on last date of the submission of the application.

Project Duration: The duration of the project is Three years and the positions are co- terminus with the duration of the project. (Initial appointment will be for one year and further extension will be granted based on annual review).

Mode of submission of application: Only online applications are to be submitted through
www.niab.org.in on or before 08 December, 2014. Link for online submission of applications will be available from 10 November 2014.

Advertisement: www.niab.org.in/Notifications/Advt_5_2014/Advt_5_2014.pdf