BOL: Related items

NovelSeq: Novel Sequence Insertion Detection

Neel — Fri, 09 Jun 2017 04:31:30 -0500

The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

http://novelseq.sourceforge.net/Home

Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

Address of the bookmark: http://novelseq.sourceforge.net/Home

IPython: Interactive notebooks

Rahul Nayak — Fri, 07 Nov 2014 12:07:02 -0600

The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.

These notebooks are normal files that can be shared with colleagues, converted to other formats such as HTML or PDF, etc. You can share any publicly available notebook by using the IPython Notebook Viewer service which will render it as a static web page. This makes it easy to give your colleagues a document they can read immediately without having to install anything.

To learn more about using the IPython Notebook, you can visit our example collection, and you can read the documentation for all the details on how to use and configure the system. The Notebook Gallery showcases many interesting notebooks covering a variety of topics, from basic programming to advanced scientific computing.

More http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261

http://ipython.org/ipython-doc/1/interactive/notebook.html

Reference http://ipython.org/notebook.html

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

medaka: Sequence correction provided by ONT Research

BioStar — Mon, 18 May 2020 16:28:00 -0500

medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.

Address of the bookmark: https://github.com/nanoporetech/medaka

NIAB Molecular Biology/Bioinformatics Scientist/RA Openings

Thu, 13 Nov 2014 13:37:27 -0600

D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Miyapur, Hyderabad, Telangana, India- 500 049

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

ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence

Abhi — Sat, 08 Jun 2024 16:03:39 -0500

ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also be able to find very large repeats in highly repetitive sequence, regardless of the size of sequence or length of repeats. ULTRA offers meaningful annotation scores and can produce annotation P-values at user request.

More at https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1

Address of the bookmark: https://github.com/TravisWheelerLab/ULTRA

Bioinformatics JRF/RA/SRF position at PANJAB UNIVERSITY

Wed, 19 Nov 2014 20:19:49 -0600

CENTRE FOR SYSTEMS BIOLOGY & BIOINFORMATICS
UIEAST, PANJAB UNIVERSITY, CHANDIGARH

Applications are invited along with complete bio-data and attested copies of certificates of qualifications, experience etc. for the one post of Research Fellow and one post of Program Assistant under PURSE Grant of the University in Centre for Systems Biology & Bioinformatics, UIEAST, Panjab University, Chandigarh which is tenable till the period of
the project.

Essential Qualification

For Research Fellow:-

M.Sc. in Systems Biology and Bioinformatics / Life Sciences with minimum 55% marks.

Preference will be given to NET/GATE/ICMR qualified candidates without fellowship however, candidates who have cleared the Panjab University Ph.D. entrance test in Systems Biology & Bioinformatics will also be eligible.

For Program Assistant:-

The candidate must have M.Sc./M.Tech/MCA/PGDCA in Computer Science and must be able to handle LAN, Linex. Preference will be given to the candidate having experience in
System Administration.

Emoluments

For Research Fellow Rs. 12,500/- per month (Fixed)
For Program Assistant Rs. 12,500/- per month (Fixed)

Applications should be reach on or before 19-11-2014 in the office of the undersigned.

Interview will be held on 21-11-2014 in the office of the Coordinator, Centre for Systems Biology & Bioinformatics, South Campus, Block-3, Sector-25, Panjab University, Chandigarh. No TA/DA will be paid.

http://jobs.puchd.ac.in/includes/jobs/2014/20141110143634-Advertisement.pdf

Bioinformatics SUB DIC (DIC)

Fri, 12 Dec 2014 21:14:57 -0600

Project Title BIOINFORMATICS SUB DIC (DIC)

Reference Number IIT/SRIC/R/DIC/2014/314, DATED 28thNovember, 2014

Temporary Position(s)

i) Junior/ Senior Project Officer (1)
ii) Junior Project Assistant (2)

Consolidated Compensation

i) Rs.16,000/- to Rs.18,000/- p.m. (depending on qualification & experience)
ii) Rs.8,000/- to Rs.10,000/- p.m. (depending on qualification & experience)

Coordinator / PI Dr. Sudip K. Ghosh, Dept of Biotechnology.

Department / Centre / School Dept of Biotechnology

Qualifications & Experience

(i) M. Sc in any branch of Life Sciences with experience in Molecular Biology/Genetics/Biochemistry preferably a Post Graduate diploma in Bioinformatics or two years working experience in bioinformatics (Minimum 60% marks starting from matriculation examination).

(ii) B. Sc. /B.A. /B. Com/Diploma in Management or Computer Science. Knowledge in computer software will be preferred (minimum 50% marks starting from matriculation examination).

More Information

Interested eligible persons may apply on plain paper, giving full bio-data along with attested copies of testimonials to the undersigned on or before 11thDecember, 2014.

Sponsor DBT, NEW DELHI

Last Date 11 Dec 2014

Application Fee Demand Draft for Rs.50/- (Not for female candidates) drawn in favour of IIT Kharagpur payable at Kharagpur

Advertisement: www.iitkgp.ac.in/topfiles/sric_job_details.php?serial=2826

Circoletto: visualizing sequence similarity with Circos

Jit — Fri, 09 Feb 2018 10:23:40 -0600

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Online version and downloadable software package for offline use (source code in PERL) freely available at http://bat.ina.certh.gr/tools/circoletto/

Contact:ndarz@certh.gr

Address of the bookmark: http://tools.bat.infspire.org/circoletto/

Internship Program for Bioinformatics / Biotechnology / MBA / MCA (No. Of Vacancy: 5)

Mon, 15 Dec 2014 08:11:02 -0600

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology / MBA / MCA students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis or marketing or software development. Applications are accepted throughout the year. Accepted students will be notified through email.