Clément Levin

What is DNA fingerprinting?

Just like your fingerprint is unique to you, the DNA sequence in your cells contains certain variations that makes it unique as well. In fact, only 0.1% of your genome differs from any other individual. DNA fingerprinting is a technique to identify individuals based on their DNA sequence. Let’s review the best method and tools in DNA fingerprinting.   What makes your DNA unique? Short tandem repeats (STRs), or minisatellites, are locations in the chromosomes that contain short and repeated nucleotide sequences. These short sequences of repetitive DNA show greater variation from one person to the next than other parts of the genome. This variation is exhibited in the number of repeated units in the sequence. Since each variant act …

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What is protein function prediction?

Identifying the function of a previously unknown protein is a difficult task. While some technologies such as RNA interference enable to assess the function of a protein experimentally, they are often labor-intensive and cannot match the rate at which new sequences and genes are being identified with high-throughput sequencing techniques.   Prediction by computational methods has thus become a privileged way of identifying new functions of unknown proteins. Here, we will briefly present the most recent methods and resources in computational protein function prediction.   Protein functions   Protein function is a wide term that includes several aspects of a protein activity. Having a common vocabulary to describe protein functions is essential for function prediction and annotation. The Gene Ontology (GO) …

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A bioinformatics tools overview

The field of bioinformatics is constantly evolving at a rapid pace. Grasping its latest developments and trends can be challenging for tool developers that wish to create accurate and up-to-date solutions that match life scientists’ needs.   Be aware of the current status of the field can be of importance for a variety of reason. For example, knowing the most popular programming language in bioinformatics can give you an advantage when applying for a position, and identifying the top tool-funding agencies can help you get the grant you need to develop your tool. For this, we created a dashboard of interactive figures to provide an overview of the field of bioinformatics tool development, accompanied with a series of blogposts to …

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Best bioinformatics software for mass-cytometry analysis

Conventional flow cytometry is limited by the number of fluorochromes and cell markers that can be targeted at once. Overcoming this limitation, mass-cytometry combines mass-spectrometry and flow cytometry by using metal-conjugated antibodies to label cellular proteins and extend the number of markers to be targeted.   A combination of spectrometry and cytometry   In mass-cytometry, antibodies are conjugated with isotopically pure elements, and these antibodies are used to label cellular proteins. Cells are nebulized and sent through an argonplasma, which ionizes the metal-conjugated antibodies. The metal signals are then analyzed by a time-of-flight mass spectrometer. The approach overcomes limitations of spectral overlap in flow cytometry by utilizing discrete isotopes as a reporter system instead of traditional fluorophores which have broad emission spectra.   Due to its numerous advantages (minimal …

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DataOnTools #6: omicX features

With more than 29,000 entities, omicX is the largest collection of bioinformatics tools. Our classification system allows to easily find and identify the tools you need. We conclude our series by providing some data analysis on the omicX collection. Tool categorization system   Software tools and database are classified in one main category among transcriptomics, genomics, phenomics, metabolomics, proteomics and epigenomics. Then, they are labelled in one or more of the 2,000 subcategories. To explore the categories, check our interactive figure (Figure 1, available online).     Obsolescence in bioinformatics tools   Tools are developed continuously, and usually hosted on institution servers and corporate websites. Eventually, their URLs will not be maintained and the tool will become inaccessible, obsolete.   omicX scans tools …

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DataOnTools #5: Tools in the literature

Scientific communications and publications are the best way to promote your work – whether you are a tool developer or a bioinformatician conducting analysis. In this article, we analyze tools publications to explore a new aspect of the evolution of the field of bioinformatics.   Tool publications and citation   In the omicX database, nearly eight out of ten have been published in a peer-reviewed journal, with 41.7% of all tools cited at least once, while 36.0% have never been cited in the literature (Figure 1a). Among those with a PMID, about half of them have never been cited in the literature, and the other half has been cited at least once. This is of importance because citations are the …

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DataOnTools #4: Evolution of tool specifications

When it comes to developing a bioinformatics software tool, many different languages can be used. Moreover, developers might have to choose on which operating systems among the most used they want their creation to be run. Finally, the target audience of the software (personal use, free distribution or commercial distribution) may influence the usage of the software (web interface, desktop, etc.).   Users can run bioinformatics software tools either on the web, locally on a desktop or server, or both. While tools that can be used on the web could be expected to be more common, reflecting the need for user-friendliness for less-skilled users, we in fact found that more than 69% of the 20,918 tools registered as software are …

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DataOnTools #3: Economics of tool development

Like any other research field, bioinformatics and software development are highly depend on funding. By extracting grants and other funding sources from tool publication, we provide a new insight on the economics of tool development.   Funding is a critical aspect of tool development. We ranked the sources of funding agencies associated with a total of 12,761 published tools to assess the top 20 tool-funding agencies worldwide (Figure 1). Nearly half of all published tools were funded by the National Institutes of Health (NIH) or the National Science Foundation (NSF), both US-based agencies.     Countries’ themselves take a critical role in funding research through national grants. Indeed figure 2 shows a high correlation (r=0.81; p<0.0001) between a country’s research …

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