ESM (Evolutionary Scale Modeling) is a family of large-scale protein language models developed by Meta AI. They’re trained on massive protein sequence databases, learning contextual representations of amino acids purely from sequence data. These representations—often called embeddings—capture both structural and functional clues.
In practice, you feed a protein sequence into ESM to obtain per-residue embeddings, which you can then use for downstream tasks like structure prediction, function annotation, or variant effect prediction. If you batch multiple sequences together, ESM aligns them by adding special start/end tokens and padding shorter sequences to match the longest one. You then slice out the valid embedding region for each protein, ignoring any padding.

Render Your Protein in Blender with Molecular Nodes

ASCP (Aspera Secure Copy Protocol) is a fast, reliable protocol for transferring large files, particularly over long distances or in conditions with network latency or packet loss. It uses a technology called fasp (Fast, Adaptive, and Secure Protocol) to maximize available bandwidth, making transfers faster than traditional methods like FTP.
For uploading data to NCBI, ASCP is particularly useful because it efficiently handles large datasets, such as genomic sequences or omics data. Its ability to resume interrupted transfers ensures that if a connection fails during an upload, the transfer continues from where it left off, saving time and bandwidth. ASCP also provides strong encryption, ensuring data security during the upload process.

Protein Dock Tools and algorithm Overview

The FoldX Suite builds on the strong fundament of advanced protein design features, already implemented in the successful FoldX3, and exploits the power of fragment libraries, by integrating in silico digested backbone protein fragments of different lengths. Such fragment-based strategy allows for new powerful capabilities: loop reconstruction, implemented in LoopX and peptide docking, implemented in PepX. The Suite also features an improved usability, thanks to a new boost Command Line Interface.

Nanopre and PacBio based Genome Assembly

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.

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try NextPolish.

IgCaller is a python program designed to fully characterize the immunoglobulin gene rearrangements and oncogenic translocations in lymphoid neoplasms. It was originally developed to work with WGS data but it has been extended to work with WES and high-coverage, capture-based NGS data.

MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer.

Whole Genome Sequencing (WGS) provides a deep insight into the DNA sequence of humans, animals, plants, and microbial genomes, with data analysis at the individual or population level. SNP/INDEL/CNV/SV and other variants of the genome can be fully analysed. Our sequencing analysis enables the identif wication of somatic and germline mutations as well as customized patterns of cancers and other diseases. (Novogene)

Learn about SeqKit, a powerful command-line toolkit designed for handling high-throughput sequencing data with ease and efficiency.

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)