BOL: Related items

KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads

Jit — Fri, 19 Jun 2020 07:34:12 -0500

KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indicates how well the assembly matches read data for each k-mer.

where, c is the count of a k-mer from reads, m is the mode of counts of read k-mers, and n is the copy of the k-mer in the assembly.

Address of the bookmark: https://github.com/liu3zhenlab/KAD

WALK-IN-INTERVIEW FOR PROJECT ASSISTANT @ BHARATHIDASAN UNIVERSITY

Mon, 12 Jan 2015 21:54:10 -0600

BHARATHIDASAN UNIVERSITY
DEPARTMENT OF BIOINFORMATICS, SCHOOL OF LIFE SCIENCES, TIRUCHIRAPPALLI – 620024

Project title: “Genome-scale metabolic modeling and simulation of rumen methanogens An in silico attempt to methane attenuation”

Funding Agency: University Grants Commission, New Delhi

Tenure of the project: Two years or till the end of the project period.

Position: Project Assistant (1 no.)

Essential qualification: First class M.Sc. in Bioinformatics/Microbiology/ Biotechnology and other related discipline.

Desirable qualification: Experience in an area relevant (Molecular Systems Engineering) to the project.

Fellowship: Rs. 5000 per month as per the UGC norms.

Upper age limit: 28 years

Date of Venue of interview: 22.01.2015, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli -620 024, Tamil Nadu

The above post is purely temporary and will be terminated with three month notice.

The Terms and the condition of the appointment shall be governed according to UGC, Govt. of India. The eligible candidates will bring their original certificates and documents at the time of interview. No TA/DA will be paid for attending the interview.

Dr. P. CHELLAPANDI
UGC-Research Awardee,
Department of Bioinformatics,
School of Life Sciences,
Bharathidasan University,
Tiruchirappalli -620 024, Tamil Nadu

Advertisement: www.bdu.ac.in/adv/PA_UGC_Bioinformatics.pdf

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

Linux operating system aimed at scientists

Pranjali Yadav — Mon, 19 Jan 2015 08:30:49 -0600

The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

Calling variants in non-diploid systems

Neel — Sat, 26 Jun 2021 15:37:49 -0500

The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes (Rebolledo-Jaramillo et al. 2014, Li et al. 2015).

Address of the bookmark: https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html

GenomeTools: The versatile open source genome analysis software

Neel — Wed, 02 Feb 2022 04:00:21 -0600

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

If you are interested in gene prediction, have a look at GenomeThreader.

http://genometools.org/pub/

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

RA Bioinformatics at CIBA

Mon, 02 Feb 2015 22:52:50 -0600

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

Research Associate – one post

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

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.

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 appear for the Walk-in-interview with original Certificate of Ph.D. / Master’s / relevant degree, passport size photograph and bio-data enclosing attested copies of educational qualification & experience certificates. TA / DA will not be paid for attending the interview.

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

Refseq viraal genome sequences !

Jit — Sat, 11 Dec 2021 08:35:18 -0600

List of all viruses on NCBI

https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

Address of the bookmark: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

JRF in Bioinformatics @ Tezpur University

Mon, 02 Feb 2015 22:50:14 -0600

Applications are invited for one temporary position of Junior Research Fellow (JRF) in the DBT Twinning Project entitled ‘In-Silico design and evaluation of sequences for γD crystalline protein’ under the Principal Investigator Dr. Anupam Nath Jha, Assistant Professor, Department of Molecular Biology and Biotechnology, Tezpur University.

Educational Qualification: Candidate must possess a M.Sc. in Bioinformatics/ Biotechnology/ Computer Science/ Physics/ Chemistry or B.Tech. or M.Tech. in Bioinformatics/ Biotechnology/ Computer Science from a recognized University/ Institute with minimum 60% marks or equivalent CGPA for general category and for SC/ST/OBC relaxation will be given as per Govt. of India rules.

Fellowship: Rs 16,000/- (Rupees sixteen thousand) only + 10% HRA per month for NET/GATE/BET/BINC qualified candidates. Rs. 12,000/- (Rupees twelve thousand) only + 10% HRA per month for other candidates.

Duration: Initially for a period of six (06) months which may be extended depending upon status of the project or until further order, whichever is earlier.

Age: Candidate should not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ ST /OBC /Women / Physically Challenged.

Interested candidates may send their application on plain paper by post along with his/her educational qualifications, recent passport/stamp size photograph and contact phone number to Dr. Anupam Nath Jha, Principal Investigator, Department of Molecular Biology and Biotechnology, Tezpur University, Napaam – 784028 or mail it to anjha@tezu.ernet.in within 20 days of publication of this advertisement.

Only shortlisted candidates will be informed by e-mail or phone for an interview. N.B. No TA/DA will be paid for attending the interview. For further details contact: Dr. Anupam Nath Jha, Assistant Professor, Principal Investigator Department of Molecular Biology & Biotechnology Tezpur University, Napaam, Tezpur-784028 (Assam)

Advertisement: www.tezu.ernet.in/ProjectWalkin/Advt-ANJ-5323-A.pdf

CrossMap: program for genome coordinates conversion between different assemblies

Rahul Nayak — Tue, 25 Jan 2022 17:59:32 -0600

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

Address of the bookmark: http://crossmap.sourceforge.net/