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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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How to use omicX statistics like a pro

omicX just launched statistics for tools, a new feature for software developers and users to get a bunch of knowledge about bioinformatics resources.   Let’s see how this will help you become a bigbio data pro!   Why it’s useful   While a few tools are being developed to address very specific needs, most of them aim at helping researchers for mainstream applications in genomics, transcriptomics, or proteomics. This leads to a lot of redundancy, and poses a problem for scientists: How to choose among several seemingly identical solutions?   The usual way of dealing with this problem is a painful, time-consuming review of the specs and literature, to optimize compatibility with other tools, or simply find the solution your …

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How to use omicX protocols like a pro

We previously discussed all the cool things you can do with the omicX search engine. Here, we’ll uncover our latest and most exciting feature, omicX protocols, so you can analyze your big biodata like a pro. What it a computational protocol   We know that the number of publications in biology is skyrocketing, and it’s becoming more and more difficult for scientists to identify the latest trends, analysis methods and tools in their field.   Searching through publications to benchmark or identify the best combination of tools for your analysis can take hours. For this reason, we developed a new feature that automatically extracts and recreates protocols (logical series of bioinformatics tools designed to perform an analysis task) from free …

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Introducing our new bioinformatics protocols

As a biologist, you probably know that the key to good data analysis is the selection and use of appropriate software. Owing to the increasing complexity of biological data, the number of tools typically required to perform an analysis is constantly growing, rendering the selection of software even more difficult. Indeed, finding the best series of tools that match your analysis criteria is challenging.   A protocol is a series of software presented in a logical order. With your data as a starting point, a protocol shows you the right pathway of tools to perform your analysis.   Until now, finding the optimal workflow was very challenging because bioinformatics analyses are difficult to decipher or remain buried in the masses of biomedical texts. To face this big …

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Choosing the right name for a bioinformatics tool

The name of your bioinformatics tool is the icing on the cake. You should be very attentive and feel concerned regarding this feature. While having a great name does not assure you to stand out, a bad appellation often results in a failure to reach your audience. The do’s and don’ts Don’t take a name that already exists Your tool is unique. As such, it deserves to have a sole name. Don’t try to copy the name of a famous tool or your favorite one. It can be detrimental for you. Indeed, people tend to compare products with each other, especially if they have the same title. They can be confused about the function of your tool.   omicX contains more …

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Best bioinformatics software for MS-based proteomics analysis

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 the OMICtools community to choose the best 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 …

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How to identify the right tools for biological data analysis

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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