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Your top 3 MS-based proteomics analysis tools

Proteomics are the next step after genomics and transcriptomics to study biological systems. However, analyzing the proteome is much more difficult than the genome or transcriptome, because each cell expresses its own set of proteins. Mass spectrometry (MS) has emerged as the most important and popular tool to identify, characterize, and quantify proteins and their post-translational modifications with high throughput and on a large scale (Zhang et al.). To help you perform your experiments in the best conditions, we asked OMICtools members to choose their favorite MS-based untargeted proteomics analysis tools. LC-MS based untargeted proteomics Two-dimension liquid-chromatography (LC) coupled with mass-spectrometry (LC-MS) is the leading technology for high-throughput proteomics. LC is used to separate proteins from different samples in parallel, and is …

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Accelerate retrieving of scientific resources with semantic search engines

  The exponential growth of the number of biological studies over the past decade has created an enormous challenge to make effective use of the accumulated information. Owing to this size, simple web-style text search engines are often not yielding the best results and a lot of important information remains buried in the masses of text (Doms, 2005). Semantic technologies have been introduced for better question answering and faster literature exploration (Doms, 2008). They use ontologies to give an overview over large query results and guide scientists for discoveries. Starting your research in biology but don’t know which platform to use to find impactful studies? Here is a list of useful resources you will love using to retrieve articles and …

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Search and find olive oil compounds with OliveNet

Olive oil is now widely recognized as a key component of the health benefits provided by the “Mediterranean diet”. However, the exact composition and biological activity of olive oil and its compounds are still being investigated. OliveNet aims at gathering all information on olive oil compounds in a knowledgebase. Here, they briefly present their database and its features.   The benefits of olive oil   The health benefits of a Mediterranean diet rich in extra-virgin olive oil was illustrated by the classical Ancel Keys Seven Countries Study and more recently the methodical, multicentre Prevention with Mediterranean (PREDIMED), trial in Spain. In the context of health benefits the initial focus was on the major mono- and poly-unsaturated fatty acids, and accumulated …

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Decipher sequencing data with file formats for NGS

Next-generation sequencing (NGS) technologies generate tremendous amount of data. A typical human genome consists of ~3 billion base pairs to be sequenced. A critical step in NGS is to extract the information, stock it and transmit it in an easy-to-use and lightweight way. Why need file format? Coded in bits, a human genome would “only” weight about 700 MB (Reid Robison). However, sequencers generate short reads that redundantly span the sequence and then need to be aligned to a reference genome. Moreover, since sequencing is not perfect, every base has a score attached to it to evaluate the quality of sequencing. Thus, file formats have been developed to code a maximum of this information in a minimum of space. Here …

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How to identify the right bioinformatics tools for your data

In the biology big data context, managing the amount and diversity of data that experiments produce is a challenging task. Depending on the scope of your research, you probably spend a lot of your time searching for the right bioinformatics tools.   Like most, you probably have a general idea of how to analyze your data and have used more than one tool. If you’re working in a computational biology laboratory, you’ve probably heard the question “What is the best software for genome sequence alignment?” or “What algorithm is the standard for sequence alignment in genetics?” While BLAST is probably the most popular tool for this, there are lots of other tools for mining, and aligning biological data.  So choosing the right solution for …

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