ImageMagick is a versatile open-source tool for image manipulation, capable of reading and writing over 200 image file formats. Renowned for its flexibility, it allows users to efficiently perform a wide array of image transformations, including resizing, format conversion, and special effects, either programmatically or via command line. Ideal for batch processing and on-the-fly image manipulation, ImageMagick is widely employed in web development, graphic design, and photography.

MGT®, the international ImMunoGeneTics information system®, is a comprehensive resource for immunogenetics and immunoinformatics. It was created and has been developed since 1989 by Professor Marie-Paule Lefranc at the Université de Montpellier, France. IMGT® is recognized as the global reference in immunogenetics and immunoinformatics due to its high-quality, integrated knowledge and its standardized nomenclature.

IgBLAST is a tool commonly used in bioinformatics. IgBLAST (Immunoglobulin BLAST) is designed for the analysis of immunoglobulin (IG) and T cell receptor (TCR) sequences. It's part of the suite of tools offered by the National Center for Biotechnology Information (NCBI).

The cellranger vdj pipeline can be used to analyze sequencing data produced from Chromium Next GEM Single Cell 5' V(D)J libraries. It takes FASTQ files for V(D)J libraries and performs sequence assembly and paired clonotype calling. The pipeline uses the Chromium Cell Barcodes (also called 10x Barcodes) and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser. Visit the What is Cell Ranger page to learn more about Cell Ranger for Immune Profiling. (10X Genomics)

SSH, or Secure Shell, is a cryptographic network protocol for secure and encrypted communication over unsecured networks. It is significant for its ability to provide secure remote access to servers, secure file transfer, and a reliable means of executing remote commands, all while ensuring the confidentiality and integrity of data in transit.

A phylogenetic tree is a branching diagram that shows the evolutionary relationships among different species or entities, based on their physical or genetic characteristics. It illustrates how species have diverged from common ancestors over time. These trees are constructed using morphological or genetic data and are used in biology, epidemiology, and conservation to understand the evolutionary history and relationships of organisms.

CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times faster than other clustering programs, for example, BLASTCLUST. Therefore it can handle very large databases, like NR. The 1st version of this program, CD-HI, was published and released in 2001. The 2nd version, called CD-HIT, was published in 2002 with significant improvements. Since 2004, CD-HIT has been hosted at bioinformatics.org as an open source project. Current CD-HIT package can perform various jobs like clustering a protein database, clustering a DNA/RNA database, comparing two databases (protein or DNA/RNA), generating protein families, and many others.

In summary, extracting information from PDB files and visualizing it with PyVista enables a deep and interactive exploration of biomolecular structures, which is vital for various scientific and medical research purposes. This approach harnesses the power of computational tools to augment our understanding of complex biological systems.

The flu NA (neuraminidase) protein is crucial because it plays a key role in the influenza virus's ability to infect host cells and spread within the body. It helps the virus to release newly formed viral particles from infected cells, facilitating the spread of the infection. As such, it's a key target for antiviral drugs and vaccine development, helping in controlling and preventing flu outbreaks.

This post provides an in-depth understanding of False Discovery Rate (FDR) and the Benjamini-Hochberg Method, crucial in statistical analysis with large datasets like genomics. It explains FDR's role in identifying false positives in multiple hypothesis testing and the Benjamini-Hochberg Method's effectiveness in controlling FDR. The post compares various p-value adjustment methods, discussing their advantages, limitations, and suitability for different data types. It emphasizes the BH method's balance in statistical power and error control, and its integration in software like R, highlighting its applicability across scientific fields.

The main idea of this work is to use PyMOL for calculating the surface information/mesh structure, and then employ Python to read that information for visualization and other complex/advanced calculations. In other words, it seamlessly bridges PyMOL and Python.

This post provides a detailed exploration of the CR9114 antibody, focusing on its binding properties and effectiveness against various influenza A virus strains. It covers the specific gene segments from which CR9114 is derived, explaining its broad reactivity to both group 1 and group 2 influenza A viruses. The article highlights the significance of the HA stem region in the virus and how CR9114's binding to this region blocks the necessary conformational changes for viral entry into host cells. Additionally, it compares CR9114 to other antibodies like CR6261 and FI6v3, discussing their different binding modes and effectiveness. The content is technical and geared towards readers with a background in biology and immunology.

In the evolving realm of biotechnology, antibodies and phage display stand as two pillars of immense significance. This article delves into the structural intricacies of antibodies, emphasizing their heavy and light chains, along with the pivotal Complementarity-Determining Regions (CDRs). Furthermore, the article illuminates the concept of phage display, a groundbreaking technique that bridges genotypic information with phenotypic expression, offering a high-throughput approach to study protein interactions. Illustrated with detailed visuals, the piece offers readers an in-depth understanding of these subjects, underscoring their paramount importance in modern medicine and research.

The blog post delves into the realm of PacBio sequencing, elucidating its significance in the world of next-generation sequencing. Contrasting PacBio with other sequencing technologies, such as Illumina's short-read and Oxford Nanopore's long-read sequencing, the article highlights the unique advantages and challenges posed by each. The comprehensive PacBio data analysis pipeline is elucidated step by step, from raw data collection to final report generation. A special section is dedicated to comparing tools used in the PacBio pipeline, offering insights into their strengths and limitations.

Gene regulation plays a crucial role in various biological processes, and understanding its mechanisms is essential for advancing our knowledge in life sciences. The Advent of ATAC-seq, a powerful tool for mapping open chromatin regions, has revolutionized the study of gene regulation by providing insight into the regulatory elements that control gene expression. This review aims to provide an overview of the current state of ATAC-seq applications in various fields, including stem cell biology, cancer research, neurobiology, immunology, plant biology, microbiology, drug discovery, personalized medicine, and synthetic biology. We discuss the advantages and limitations of ATAC-seq and highlight its potential for identifying new therapeutic targets and developing personalized therapies. Overall, ATAC-seq has proven to be a valuable tool for unlocking gene regulation and has the potential to lead to significant breakthroughs in many areas of life science research.