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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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A guide for protein structure prediction methods and software

To exert their biological functions, proteins fold into one or more specific conformations, dictated by complex and reversible non-covalent interactions. Determining the structure of a protein can be achieved by time-consuming and relatively expensive technics such as crystallography, nuclear-magnetic resonance spectroscopy, and dual polarization interferometry. Bioinformatics software have been developed to compute and predict protein structures based on their amino acid sequences.   A recap on protein structure   As an alternative to experimental technics, structure analysis and prediction tools help predict protein structure according to their amino-acid sequences. Solving the structure of a given protein is highly important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). The field of computational …

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Evaluate the quality of your read alignment with GeneQC

RNA-sequencing has replaced gene array and is now the leading technology in gene expression analysis. After a sequencing step, reads need to be mapped to a reference genome. However, this step is not perfect and errors can impact all downstream analyses. To address this issue, Adam McDermaid and colleagues have developed GeneQC, a tool to evaluate the quality of read alignment. Here, he describes GeneQC and its features. Quality control of read alignment One of the main benefits of using modern RNA-Sequencing (RNA-Seq) technology is the more accurate gene expression estimations compared with previous generations of expression data, such as the microarray. However, numerous issues can result in the possibility that an RNA-Seq read can be mapped to multiple locations …

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Evaluating biomedical data production with text mining

Evaluating the impact of a scientific study is a difficult and controversial task. Recognition of the value of a biomedical study is widely measured by traditional bibliographic metrics such as the number of citations of the paper and the impact factor of the journal.   However a more relevant critical success criteria for a research study likely lies in the production itself of biological data, both in terms of quality and also how these datasets can be reused to validate (or reject!) hypotheses and support new research projects. Although biological data can be deposited in specific repositories such as the GEO database, ImmPort, ENA, etc., most data are primarily disseminated in articles within the text, figures and tables. This raises the question – how …

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Upgrade your search experience

High throughput technologies are generating increasingly vast amounts of biological data streams. Thousands of new bioinformatics tools have been designed for their management and analysis. Finding the appropriate program for a specific need is typically a challenging and time-consuming task. Find the right answer for your biological data analysis OMICtools addresses this challenge and empowers you to locate and access information for more than 17,000 software tools and databases in a single place. Manually curated and updated, OMICtools resources are methodically organized in a didactic hierarchical classification. The number of available tools is constantly growing. From more than 1,100 categories, you can easily retrieve a relevant list of tools which precisely relate to a specific step of data analysis for the biotechnology …

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