BRC Tools and Services
The BRCs include a wide array of tools and services to enable researchers to locate, filter, process, analyze, and explore data. Note that many of these tools require login to the BRC to enable use with private data.
Tools for Viruses at IRD/ViPR
| Identify Similar Sequences (BLAST) | Uses BLAST algorithms to identify similar nucleotide or amino acid sequences in a variety of custom BRC databases. |
| Identify Short Peptides in Proteins | Identifies short amino acid strings in target proteins using exact, fuzzy, or pattern matching. |
| Generate Phylogenetic Tree | Generates phylogenetic trees based on nucleotide or amino acid sequences and displays results in interactive tree viewer to annotate tree nodes. |
| Identify Point Mutations | Identifies protein sequences that have a specific amino acid at a specific position. |
| Pandemic H1N1 Classification | Identifies nucleotide sequences closely related to the 2009 pandemic H1N1 strain. |
| HPAI H5N1 Clade Classification | Predicts clade for highly pathogenic H5 HA sequences. |
| Swine H1 Clade Classification | Predicts clade for Global and US Swine H1 viruses. |
| Sequence Format Conversion | Performs simple sequence format conversions |
| HA Subtype Numbering Conversion | Renumbers HA sequences according to a cross-subtype numbering scheme proposed by Burke and Smith. |
| Align Sequences | Aligns nucleotide or amino acid sequences. |
| Visualize Aligned Sequences | Displays interactive alignment viewer to view aligned nucleotide or amino acid sequences. |
| Annotate Sequences | Identifies segment, type, CDS location, and subtype (if segments 4 or 6), and possible sequencing errors for a given set of FASTA sequences using IRD Influenza annotation protocol. |
| VIGOR4 Genome Annotator (ViPR) | Annotates given genome sequence using VIGOR4 (Viral Genome ORF Reader). |
| GATU Genome Annotator (ViPR) | Annotates given genome sequence using a well annotated reference genome. |
| Analyze Sequence Variation (SNP) | Computes the extent of variation at each position of nucleotide or amino acid sequences uploaded or selected from the BRC database. |
| Metadata-driven Comparative Analysis Tool for Sequences (meta-CATS) | Performs a customized automated comparative analysis to identify positions in the sequence that significantly differ between groups of sequences |
| PCR Primer Design | Predicts the optimal primer set(s) for DNA sequences |
| Antiviral Resistance Risk Assessment | Determines the presence of amino acid changes associated with altered response to antiviral drugs in user input sequence. |
| Identify Sequence Features in Segments | Identifies experimentally characterized sequence features or phenotypic variant types. |
| SARS-Cov-2 Genome Assembly and Annotation (via BV-BRC) | Provides meta-service that performs tailored genome assembly, annotation, and variation analysis of SARS-CoV-2 genome reads. |
Tools for Bacteria at PATRIC
| BLAST | Performs searches against public or private genomes in the BRC or other reference databases using DNA or protein sequences. |
| Codon Tree | Constructs custom phylogenetic trees built from up to 100 genomes using the Codon Tree method. |
| Comparative Pathway | Identifies a set of pathways based on taxonomy, EC number, pathway ID, pathway name and/or specific annotation type across a set of genomes. |
| Comprehensive Genome Analysis | Provides meta-service including genome assembly, annotation, nearest neighbors, subsystem summary, phylogenetic tree, and distinguishing features. |
| Differential Expression | Integrates user-provided differential expression datasets for comparison with other data sets or analysis using annotations. |
| FastqUtils | Performs operations on FASTQ files including base call quality reports, read alignment to genomes, quantity/quality assessment, and trimming. |
| Genome Alignment | Produces a whole-genome alignment of two or more genomes and presents a visualization showing homologous regions and rearrangements |
| Genome Annotation | Annotates prokaryotic genomes with gene calls, protein features, and a variety of other genomic features. |
| Genome Assembly | Assembles sequence reads into contigs with a variety of assembly algorithms tuned to fit certain data types or analysis criteria |
| ID Mapper | Maps BRC identifiers to those from other prominent external databases such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc, and vice versa. |
| Metagenome Binning | Bins reads or contigs from environmental samples into a set of genomes to reconstruct constituent bacterial and archaeal genomes. |
| Metagenomic Read Mapping | Aligns reads against antibiotic resistance genes, virulence factors, or other custom sets of genes. |
| Model Reconstruction | Generates draft genome-scale metabolic models using genome annotation and a collection of other analytical methods. |
| Protein Family Sorter | Displays the distribution of protein families across a set of selected genomes via an interactive heatmap with clustering and filter controls. |
| Proteome Comparison | Compares up to eight genomes against a reference by identifying corresponding protein sequences, displayed in an interactive circular genome view. |
| RNASeq Analysis | Provides services for aligning, assembling, and testing differential expression on RNA-Seq data from bacterial or host, e.g., human. |
| Similar Genome Finder | Finds similar public genomes in the BRC database or computes genome distance between genomes. |
| Taxonomic Classification | Assigns reads or contigs from metagenomic samples to taxonomic bins, providing an initial profile of the possible constituent organisms present in the sample |
| TnSeq Analysis | Facilitates determination of essential regions in bacterial genomes from transposon insertion sequencing (Tn-Seq) data |
| Variation Analysis | Identifies and annotates sequence variations in short read samples and compares them to a closely related reference genome. |
Tools for Eukaryotes/Vectors at VEuPathDB
| BLAST | Finds genes, genomic sequences, ESTs, or PopSet Sequences that have sequence similarity to given input sequence. |
| Companion | Provides parasite genome annotation as a service using a reference-based approach. |
| EuPaGDT (Eukaryotic Pathogen CRISPR gRNA Design Tool) | Identifies guide RNA (gRNA) in input gene(s) to guide appropriate gRNA design for many eukaryotic pathogens. |
| Galaxy | Analyzes RNA-Seq, ChIP-Seq, Variants, and many other data sets with preconfigured workflows and preloaded genomes. |
| PubMed and Entrez | Provides targeted search results from PubMed and Entrez. |
| Sequence Retrieval | Retrieve FASTA sequences based on provided identifiers. |
| Web Services | Provides programmatic access to searches via REST Web Services, returning a list of records (genes, compounds, etc.) in selected formats. |
| Enrichment Analyses | Provides a tool to determine statistical enrichment in gene lists of gene ontology (GO) terms, metabolic pathways and text in gene product descriptions. |
| Boolean operations | Provides a tool to combine search results using Boolean operations like intersect, union and minus. |
| Apollo | Provides a tool to enable the annotation of both functional and structural aspects of genes. |
| Site Search | Provides a tool to search the entire site for any keyword. Search results are organized in filterable categories. |
| Genome Browser | Provides a tool to explore genomes and aligned genomic data in an interactive browsable way. |
| User Comments | Provide a mechanism for users to quickly share their knowledge about genes with the community. |
| Multiple sequence alignment (isolates) | Provides a multiple sequence alignment tool for nucleotide sequences retrieved from PopSet. |
| Results downloads | Provides a tool to customize downloads with any available information. |
| Data analysis searches | Specialized searches enabling sophisticated mining of underlying data. |
| --- Annotation | Provides a set of searches that enable the identification of genes based on lists of IDs, user comments and annotation updates. |
| --- Epigenomics | Provides searches to identify genes based on location of epigenetic markers. |
| --- Function prediction | Provides searches to identify genes based on predicted function using enzyme commission (EC) numbers or GO terms. |
| --- Gene models | Provides a tool to identify genes based on their type and/or structural features. |
| --- Genetic variation | Provides a tool to identify genes based on genetic variation in the population, including single nucleotide polymorphisms or copy number variation. |
| --- Genomic Location | Provides a tool to identify genes based on their location on nuclear or non-nuclear genomes. |
| --- Immunology | Provides a tool to identify genes whose protein products are predicted to contain epitopes identified by the Immune Epitope Database and Analysis Resource (IEDB). |
| --- Orthology and synteny | Provides tools to identify genes based on their phyletic pattern across the tree of life. |
| --- Pathways and interactions | Provides tools to identify genes based on their involvement in metabolic pathways or their interaction with other genes. |
| --- Phenotype | Provides a tool to identify genes based on available phenotype datasets. |
| --- Protein features and properties | Provides tools to identify genes based on the properties of the proteins they code for such as molecular weight, isoelectric point or presence of InterPro domains. |
| --- Protein targeting and localization | Provides tools to identify genes based on predicted elements that may determine their subcellular localization such as signal peptides and transmembrane domains. |
| --- Proteomics | Provides tools to identify genes based on experimental proteomic data including mass spectrometry and quantitative data. |
| --- Sequence analysis | Provides tools to identify genes based on specified analyses such as regular expressions to define motifs |
| --- Structure analysis | Provides tools to identify genes based on structural analyses. |
| --- Taxonomy | Provides a tool to identify genes based on their taxonomy. |
| --- Transcriptomics | Provides tools to identify genes based on experimental transcriptomic data including expressed sequence tags, microarrays or RNA sequencing. |
| --- Popset Isolate Sequences | Provides tools to identify isolates retrieved from the PopSet database using information about the isolates or by sequence similarity. |
| --- Genomic Sequences | Provides tools to retrieve genomic sequences such as contigs, scaffolds or chromosomes |
| --- Genomic Segments | Provides tools to identify specific segments in the genomic sequence by location or regular expressions. |
| --- Single Nucleotide Polymorphisms (SNPs) | Provides tools to find SNPs identified from next generation sequencing data that distinguish specified populations. |
| --- Expressed Sequence Tags (ESTs) | Provides tools to identify ESTs retrieved from dbEST. |
| --- Metabolic Pathways | Provides tools to identify metabolic pathways and to dynamically interact with pathways. |
| --- Compounds | Provides tools to identify substrates and reactants found in metabolic pathways. |