BOL: Related items

DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms

Neel — Wed, 25 Nov 2020 19:51:38 -0600

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

Address of the bookmark: http://www.ub.edu/dnasp/

Studentship

Tue, 24 Jan 2017 04:26:14 -0600

Advt. No. ACBR/BTBI/BIF/Manpower/ADV/16-17
Research Associate/ Studentship/ Traineeship Jobs opportunity in University of Delhi - Dr. B.R. Ambedkar Center for Biomedical Research (ACBR) on temporary basis
Studentship
No. of Post : 01
Qualifications : Applicants who are pursuing Post Graduate Degree course/ Diploma in Bioinformatics/ Biomedical Sciences/ Biotechnology/Life Sciences/Chemistry/ Biochemistry with a programme in Bioinformatics to carry out the project.
Remuneration : Rs. 8,000/-
Traineeship
No. of Post : 01
Qualifications : Applicants who have completed their Post Graduate degree in Bioinformatics /Biomedical Sciences/Biotechnology/Life Sciences/Chemistry/Biochemistry or any other branch of Life Sciences with knowledge in Bioinformatics
Remuneration : Rs. 8,000/-
Research Associate
No. of Post : 01
Qualifications : Ph.D. in Bio-Medical Sciences/Bioinformatics/ Biotechnology/Life Sciences/ Chemistry/ Bio-Chemistry and related areas
Remuneration : Rs. 36,000/-

Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in; mchopradu@gmail.com.
Interview Date : 13.02.2017
Time : 10:00 am-12:00 noon
Venue : ACBR

Calculate the significance of the difference between two trends

BioStar — Tue, 14 Mar 2023 05:41:53 -0500

To calculate the significance of the difference between two trends, you can use a statistical test such as a t-test or ANOVA (analysis of variance). Here are the general steps to follow:

Define your null hypothesis (H0) and alternative hypothesis (H1). For example, H0 might be that there is no significant difference between the two trends, while H1 might be that there is a significant difference.
Collect data on the two trends. Make sure that the data is independent, normally distributed, and has equal variances.
Calculate the means and standard deviations of each trend.
Calculate the test statistic using a t-test or ANOVA. The test statistic will depend on the specific test you choose, but it will generally compare the difference in means between the two trends to the variability within each trend.
Determine the p-value associated with the test statistic. The p-value represents the probability of obtaining a test statistic as extreme as the one you calculated, assuming that the null hypothesis is true.
Compare the p-value to your chosen significance level (usually 0.05 or 0.01). If the p-value is less than or equal to the significance level, reject the null hypothesis and conclude that there is a significant difference between the two trends. If the p-value is greater than the significance level, fail to reject the null hypothesis and conclude that there is not enough evidence to support a significant difference.

It's important to note that the specific details of each step will depend on the type of test you choose and the software you use to perform the analysis.

The most common methods for comparing means include:

Methods	R function	Description
T-test	t.test()	Compare two groups (parametric)
Wilcoxon test	wilcox.test()	Compare two groups (non-parametric)
ANOVA	aov() or anova()	Compare multiple groups (parametric)
Kruskal-Wallis	kruskal.test()	Compare multiple groups (non-parametric)

iTOL: interactive Tree Of Life

Jit — Tue, 31 Jan 2017 05:56:30 -0600

Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

Address of the bookmark: http://itol.embl.de/

Important Journals, Blogs and Forums for Bioinformaticians

Jit — Wed, 08 Feb 2017 09:15:31 -0600

Journals. Most journals have RSS feeds for their current updates.

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

The OpenHelix Blog
Ensembl blog
Galaxy News
Blue Collar Bioinformatics
Homologus
Golden Helix - our 2 SNPs
Genomics Law Report
R-bloggers (aggregates feeds from >350 blogs about R)
Genomes Unzipped
Jason Moore's Epistasis Blog
23andMe - the Spitoon

Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
Enseqlopedia: James Hadfield’s blog on all things NGS.
Epistasis Blog: Jason Moore’s computational biology blog.
RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
RNA-Seq Blog: Transcriptome Research & Industry News.
The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

ONT assembly and Illumina polishing pipeline

Jit — Thu, 23 Nov 2017 10:13:42 -0600

This pipeline performs the following steps:

Assembly of nanopore reads using Canu.
Polish canu contigs using racon (optional).
Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

JRF Bioinformatics job vacancies in Tezpur University

Tue, 14 Feb 2017 16:40:26 -0600

Memo No. DoRD/CSE/SSS/20-295/112-A Date: 01/02/2017

Project Title : Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

Rahul Nayak — Sat, 02 Dec 2017 18:25:44 -0600

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en
You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

Postdoctoral Research Position in Bioinformatics in Milan

Thu, 20 Apr 2017 12:53:12 -0500

The lab of Immunobiology of Neurological Disorders has a main interest in the biological processes associated with multiple sclerosis, an inflammatory disorder of the central nervous system. The projects of interest for this application involve research on translational bioinformatics in complex human neurological disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
Salary will depend on qualification and experience. Starting date: immediate.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability

4. 2-3 contact names

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/