The omicX blog

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 …

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) …

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 …

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 …

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 …