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http://www.sanbi.ac.za/resources/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research

Proper citation: South African National Bioinformatics Institute: Resources (RRID:SCR_001867) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/HTGS/

Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

Proper citation: High Throughput Genomic Sequences Division (RRID:SCR_002150) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/genre/proj/yeast/index.jsp

The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.

Proper citation: CYGD - Comprehensive Yeast Genome Database (RRID:SCR_002289) Copy   

•   Source: SciCrunch Registry

http://microbes.ucsc.edu/cgi-bin/hgGateway?db=neisMeni_MC58_1

Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)

Proper citation: Neisseria meningitidis MC58 Genome Page (RRID:SCR_002200) Copy   

•   Source: SciCrunch Registry

http://insulatordb.uthsc.edu/

A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search.

Proper citation: CTCFBSDB (RRID:SCR_002279) Copy   

•   Source: SciCrunch Registry

http://www.ark-genomics.org/

Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners.

Proper citation: ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) Copy   

•   Source: SciCrunch Registry

http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genome

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

Proper citation: NCBI Genome (RRID:SCR_002474) Copy   

•   Source: SciCrunch Registry

https://cghub.ucsc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.

Proper citation: Cancer Genomics Hub (RRID:SCR_002657) Copy   

•   Source: SciCrunch Registry

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

https://github.com/ruanjue/wtdbg2.git

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

Proper citation: WTDBG (RRID:SCR_017225) Copy   

•   Source: SciCrunch Registry

https://github.com/theaidenlab/3d-dna.git

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

Proper citation: 3D de novo assembly (RRID:SCR_017227) Copy   

•   Source: SciCrunch Registry

https://github.com/josephryan/matemaker

Software tool to make artificial mate pairs from long sequences for scaffolding.

Proper citation: matemaker (RRID:SCR_017199) Copy   

•   Source: SciCrunch Registry

https://www.drive5.com/piler/

Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.

Proper citation: PILER (RRID:SCR_017333) Copy   

•   Source: SciCrunch Registry

https://github.com/BDI-pathogens/phyloscanner

Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.

Proper citation: phyloscanner (RRID:SCR_017400) Copy   

•   Source: SciCrunch Registry

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) Copy   

•   Source: SciCrunch Registry

https://github.com/tanghaibao/mcscan

Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format.

Proper citation: MCScan (RRID:SCR_017650) Copy   

•   Source: SciCrunch Registry

https://blobtools.readme.io/docs

Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants.

Proper citation: Blobtools (RRID:SCR_017618) Copy   

•   Source: SciCrunch Registry