Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated.

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).

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 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.

VS Code is a free, open-source code editor developed by Microsoft. It provides a range of features for editing, debugging, and version control, including support for multiple programming languages, extensions for customization, and a built-in terminal. Who sad this?

RNA structure research is important for understanding RNA function and regulation, as the structure of RNA molecules can impact their interactions with other molecules, such as proteins and small molecules, and influence gene expression and protein synthesis. Who sad this?

Chip-Seq, Know to Unknown = =

Unmapped reads Annotations

DNA Seq Pipelines and tricks

This post would show you a pipeline to find the new or abnormal transcript isoforms after de-novo by Trinity

Tricks for dealing with VCF files

If you need a fancy but elegant calendar live in your terminal, khal would be an awesome choice.

Different kinds of apps/software collection for Linux mainly, you may never know that Linux can't down so much of things!

Pymol: the best protein structure viewer