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bioinformaticslife sciencesmetagenomicsopen source softwareproteinprotein folding
The Steinegger Lab Dataset comprises biological databases and resources critical for protein sequence and structure analysis, developed to support ColabFold, MMseqs2, and Foldseek/Foldcomp—three high-performance computational tools widely used in bioinformatics.The MMseqs2 dataset serves as the backbone for our fast structure prediction tool, ColabFold, and includes UniRef30, BFD, and the ColabFold environmental databases. These datasets are specifically designed for the rapid generation of multiple sequence alignments (MSAs), which are essential for high-accuracy structure prediction. Beyond ...
fastageneticgenomiclife sciencesmetagenomicsSTRIDEStranscriptomicswhole exome sequencingwhole genome sequencing
This repository is a re-analysis of the NCBI Sequence Read Archive (SRA), December 2023 freeze, to make it more accessible. The SRA is an open access database of biological sequences, containing raw data from high-throughput DNA and RNA sequencing platforms. It is the largest database of public DNA sequences worldwide, containing a wealth of genomic diversity across all living organisms. This repository contains Logan, a set of compressed FASTA files for all individual SRA accessions, in the form of unitigs and contigs. Borrowing methods from the realm of genome assembly, unitigs preserve near...
benchmarkbioinformaticslife sciencesmetagenomicsmicrobiome
Database for use with Kraken2 (taxonomic annotation of metagenomic sequencing reads) including all NCBI RefSeq genomes available in release V205
bioinformaticsbiologyecosystemsenvironmentalgeneticgenomichealthlife sciencesmetagenomicsmicrobiome
QIIME 2 (pronounced “chime two”) is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported.
amino acidfastafastqgeneticgenomiclife sciencesmetagenomicsmicrobiome
The NIH-funded Human Microbiome Project (HMP) is a collaborative effort of over 300 scientists from more than 80 organizations to comprehensively characterize the microbial communities inhabiting the human body and elucidate their role in human health and disease. To accomplish this task, microbial community samples were isolated from a cohort of 300 healthy adult human subjects at 18 specific sites within five regions of the body (oral cavity, airways, urogenital track, skin, and gut). Targeted sequencing of the 16S bacterial marker gene and/or whole metagenome shotgun sequencing was performe...
bioinformaticsgeneticgenomiclife sciencesmetagenomicsviruswhole genome sequencing
Preprocessed databases for use with the Hecatomb pipeline for viral and phage sequence annotation.
bioinformaticsbiologygenomiclife sciencesmetagenomicsmicrobiomereference indexwhole genome sequencing
This dataset comprises pre-built indexes for the bioinformatics software Kaiju, which is used for taxonomic classification of metagenomic sequencing data. Various indexes for different source reference databases are available.
SocialGene RefSeq Databases
amino acidbioinformaticschemical biologygenomicgraphmetagenomicsmicrobiomepharmaceuticalprotein
Precomputed SocialGene Neo4j graph databases of various sizes built from RefSeq genomes and MIBiG BGCs.
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Usage examples
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