BOL: Related items

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

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/

Complete genome sequence of Wuhan seafood market pneumonia virus is out !

Jit — Fri, 31 Jan 2020 02:36:59 -0600

Wuhan-Hu-1 claimed at least 40 lives and infected at least 1300 others in China. Cases are now being reported from Thailand, Singapore, Malaysia, South Korea, Japan, Vietnam, Nepal, France, Australia and even as far as the US. On Jan 10 2020, while news of the first fatality was barely trickling in, the 29,903 letters constituting the viral genome from an affected individual in Wuhan had already been elucidated (even though a few corrections were made subsequently). All the viral genome sequences from affected individuals are very very close to each other. Several are identical and none has more than 5 differences (99.983% similarity). This strongly suggests that transmission into humans came from a single pointed source and happened very recently, between Sep-Dec 2019.

Check out the detail at https://www.ncbi.nlm.nih.gov/nuccore/MN908947

JRF in Bioinformatics @ NEHU

Tue, 20 Jan 2015 22:57:49 -0600

Department of Botany & Bioinformatics Centre
NORTH-EASTERN HILL UNIVERSITY, SHILLONG 793022

Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (2) and Project Assistant (1) in

DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(2 nos.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/Biochemistry/ Biotechnology/ Bioinformatics; Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science, Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned
within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service.

Advertisement: www.nehu.ac.in/Advertisements/BICAdvtPV_200115.pdf

Submit your SARS-CoV-2 sequence data to GenBank

Neel — Thu, 09 Apr 2020 18:28:25 -0500

Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/

Quickly and easily add your SARS-CoV-2 sequence data to the growing public archive with new, special features and support from NCBI. new SARS-CoV-2 sequence submission landing page will help you get started. GenBank submissions are accessioned and released in approximately 1-2 working days, and Sequence Read Archive (SRA) submissions typically processed and released within hours. Submission is simple!

More information is available on NCBI Insights. https://ncbiinsights.ncbi.nlm.nih.gov/2020/04/09/sars-cov2-data-streamlined-submission-rapid-turnaround/

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

Mon, 12 Jan 2015 01:39:45 -0600

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)
9 - 14 August 2015 St. Augustine, Trinidad and Tobago

Organiser: Christine Carrington (University of the West Indies - UWI, St. Augustine, Trinidad and Tobago)
Co-organisers: Anne-Mieke Vandamme, Philippe Lemey (Katholieke Universiteit Leuven, Belgium), Marco Salemi, Mattia Prosperi (University of Florida, Gainesville, USA) and Karen E. Nelson (J. Craig Venter Institute, Rockville, USA)

Requests for information directly to:
Christine Carrington
Department of Preclinical Sciences
Faculty of Medical Sciences
University of the West Indies (UWI)
St. Augustine
Trinidad and Tobago
Telephone: +1-868-6452640 ext. 5009, +1-868-6848803
Fax: +1-868-6621873
E-mail: veme2015@sta.uwi.edu

Deadline for receipt of applications by local organiser: 15 March 2015
CALL FOR APPLICATIONS NOW OPEN
http://www.icgeb.org/course-application-trinidad-and-tobago-2015.html

http://rega.kuleuven.be/cev/veme-workshop/2015

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Manisha Mishra — Mon, 18 Jan 2021 10:47:56 -0600

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

WuXi has acquired NextCODE Health

Pranjali Yadav — Mon, 19 Jan 2015 08:17:35 -0600

Shanghai, China-headquartered pharmatech company WuXi (NYSE: WX) has acquired NextCODE Health, a genomic analysis and bioinformatics company based in the USA.

The acquisition was made for $65 million in cash, and WuXi plans to merge its genome center with NextCODE Health to form a new company, WuXi NextCODE Genomics. The business will be headquartered in Shanghai and have operations in Cambridge, Massachusetts, and Reykjavik, Iceland.

With the huge unmet medical needs in diseases with a genetic component and the rapid advances in genomics and bioinformatics, now is the right time for WuXi to make a strategic investment in this field, and NextCODE is the right partner. This new venture of WuXi NextCODE Genomics will create important new genomic and bioinformatic products and services to help make personalized treatment and medicine a reality. It will also enable doctors to provide better treatments to patients.

The complete sequence of a human genome

Neel — Thu, 31 Mar 2022 23:58:18 -0500

The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

RA Bioinformatics at CIBA

Fri, 13 Feb 2015 11:23:18 -0600

Recruitment The following posts are to be filled purely on temporary basis under CIBA Component of “Centre for Agricultural Bioinformatics (CABin)” project at this Institute.

Posts Research Associate

Date & Time of Interview 18th Feb 2015 at 10.00 a.m.

Project Name “Centre for Agricultural Bioinformatics (CABin)”

Duration 12th Plan (2012-2017) / co-terminus with the project 12th Plan (2012-2017) / co-terminus with the project

Essential Qualification Ph.d / M.Sc./ M.Phil (Bioinformatics) With 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience in the relevant subject.

Technician

B.Tech. or Master degree in computer science/Computer Engineering /MCA or equivalent. Desirable qualification: Experience in Java/ C++/ PHP/ PERL/ Python etc. based application development using Linux, Apache and MySQL/Oracle.

Emoluments Rs.24000/- p.m. + 30% HRA for Ph.D holders / Rs.23000/- p.m. + 30% HRA for Master Degree holders A consolidated pay Rs.25000/- per month.

Age Limit Maximum 40 years for men and 45 years for women as on date of interview.

Age limits are relaxable for SC / ST / OBC candidates as per rules.

Maximum 40 years for men and 45 years for women as on date of interview.

Age limits are relaxable for SC / ST / OBC candidates as per rules.

Eligible Candidates may send their Curriculum Vitae along with the contact numbers to ashok@ciba.res.in on or before 13-02-2015.

Candidates selected after initial screening will be called for interview.

Advertisement: www.ciba.res.in/attachments/jobs/CABin-3006.pdf