Find more at http://www.imtech.res.in/raghava/

• In a GitHub or GitLab repository
• Free to use
• Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

No.: SPU/CISST/Advt./2014-15/519

ADVERTISEMENT for Teaching Positions (Contractual)

Applications for the following Contractual Teaching Position are invited for Centre for Interdisciplinary Studies in Science and Technology (CISST), Sardar Patel University:

2. Assistant Professor (ONE) (Contractual)

For the subject of Bioinformatics

Qualifications:

(I) Good academic record as defined by the concerned university with at least 55 % marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master’s level

(II) Ph.D. degree in the concerned subject or in a relevant interdisciplinary subject
from an Indian University or NET/SLET clearance Contractual appointment carries a total Fixed Emoluments of Rs. 30,000/- p.m without any assurance of permanent Positions and related benefits.

An Application Form in prescribed Performa, available on University Website: www.spuvvn.edu should be filled in completely in Twelve Copies with self attested copies of certificates of qualifications and experience. Only one copy of each mark sheet be attached with the first copy of the application form. All 12 (Twelve) Application forms should be sent to Registrar’s office along with Demand Draft of Application form fee of Rs. 250/- (Non-refundable) in favour of “REGISTRAR, SARDAR PATEL UNIVERSITY, VALLABH VIDYANAGAR”. The S.C. and S.T. category candidates need not to pay Application fee.

Applicants who are in service should apply through their present employers. Candidates called for interview shall be required to attend at their own cost.

In absence of suitable candidate, the University may relax the eligibility criteria, for conditional appointment.

The last date of receipt of application by the University is 30th April, 2014

Advertisement: www.spuvvn.edu/careers/CISST%20Advt.%20April%202014.pdf

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

Basic Galaxy Tutorial

• RNA-Seq tutorial based on Trapnell et al. (2012) Nature Protocols

In this tutorial we cover the concepts of RNA-Seq differential gene expression (DGE) analysis using a very small synthetic dataset from a well studied organism.

Advanced Galaxy Tutorial

• RNA-Seq (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based differential expression tools:

* CuffDiff

* EdgeR

* DESeq2

Advanced Command Line Tutorial

• Graphical Output with CummeRbund introduces some basic commands using the cummeRbund package of the R programming language

You will need to install R, RStudio and cummeRbund on your PC (explained in the Tutorial). You will learn how to produce graphical output from RNA-Seq analysis previously done using a Cuffdiff analysis.

Variant Detection

Basic Galaxy Tutorial

• Variant Detection tutorial

In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.

Advanced Galaxy Tutorial

• Variant Detection (Advanced) Tutorial

In this tutorial we compare the performance of three statistically-based variant detection tools:

* SAMtools: Mpileup

* GATK: Unified Genotyper

* FreeBayes

Each of these tools takes as its input a BAM file of aligned reads and generates a list of likely variants in VCF format

Pipelines are for those who are comfortable with using the UNIX command line; and often allow more control over branching and iteration logic.

• WGS/exome GATK-based variant calling pipeline

This is a basic variant-calling and annotation pipeline developed at the Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne. It is based around BWA, GATK and ENSEMBL and was originally designed for human (or similar) data. The master branch is configured for WGS data; there is an exome branch configured for variant calling in exome data.

To run the pipeline you will need Rubra: https://github.com/bjpop/rubra. Rubra uses the python Ruffus library: http://www.ruffus.org.uk/.

Protocols

• Familial Variant Calling

In this protocol we discuss and outline the process of calling familial related mutations.

• Somatic Variant Calling

In this protocol we discuss and outline the process of identifying somatic variants or mutations.

Assembly

Basic Galaxy Tutorial

• Genome assembly tutorial

In this tutorial we carry out de novo assembly of a microbial genome. We have also written a De novo Genome Assembly for Illumina Data Protocol for a more generic description of the method.

Protocol

• De novo Genome Assembly for Illumina Data

In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. Use our Genome assembly tutorial to learn a specific case of using Galaxy to carry out de novo assembly of a microbial genome.

Small RNAs

Basic Galaxy Tutorial

• Quality control for small RNA

This tutorial covers initial steps of the workflow for analysis of short RNA expression such as a quality control of the raw reads, processing of the raw reads for the subsequent analysis and initial quality assessment of the library.

ChIP Seq

Protocol

• ChIP-Seq

In this protocol we discuss ChIP-Seq: a method to analyze the interaction between proteins and DNA.

Amplicons

Protocol

• Amplicon Alignment

In this protocol we discuss and outline the process of aligning custom amplicons using primers for high precision.

Learn Galaxy

Introduction to Galaxy, for those who are very new to Galaxy.

Using Histories and Workflows, for those with some Galaxy knowledge.

The Galaxy project website has many tutorials and screencasts about using Galaxy and the tools, and developing new tools.

Address of the bookmark: https://genome.edu.au/wiki/Learn

Please report new whole genome alignment tools under comment sections.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2