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PSI-BLAST / Position-Specific Iterated Basic Local Alignment Search Tool
Allows to find regions of sequence similarity. PSI-BLAST is a protein database search program. The software is able to access the probable substitutions at each sequence position using the results of a previous Gapped-Blast search, an algorithm comparing the amino acid substitution matrix. It can combine search results with robust statistics to build and apply profiles also known as a position-specific scoring matrix. A modified application of PSI-BLAST - PSI-BLASTexB - that solves sequence weighting scheme limitations, was also developed.
RDP / Ribosomal Database Project
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Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along with tools to allow researchers to analyse their own rRNA gene sequences. RDP offers tools for browsing and searching the data collections, for taxonomic classification and nearest neighbour search, for primer-probe testing and for tree building. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics.
Blast2GO
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Permits functional annotation, management, and data mining of novel sequence data. Blast2GO is based on the utilization of common controlled vocabulary schemas, the gene ontology (GO). It takes in consideration similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. This tool is suitable for plant genomics research. It generates functional annotation and assesses the functional meaning of their experimental results.
PICRUSt / Phylogenetic investigation of communities by reconstruction of unobserved states
A computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty.
GuideScan
Allows for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. Rather than using an alignment tool, GuideScan uses a retrieval tree (trie) data structure, which efficiently and precisely enumerates all targetable sequences present in a given genome. Traversals of the trie allow for the computation of sequence mismatch neighborhoods, which are used to construct databases of gRNAs whose target sites are unique in the genome up to a user-defined number of mismatches. The GuideScan website allows users to input coordinates of genomic features in batch, to choose between designing single internal gRNAs or pairs of flanking gRNAs, and retrieve for each genomic coordinate a pre-defined number of gRNAs or gRNA pairs.
BioMart
Integrates BioMart data resources with data analysis software in Bioconductor. BiomaRt can annotate a wide range of gene or gene product identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and Online Mendelian Inheritance in Man (OMIM) annotation. Furthermore, biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases. The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.
antiSMASH / antibiotics & Secondary Metabolite Analysis Shell
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Aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters. antiSMASH facilitates the mining of bacterial and fungal genomes. It includes gene cluster boundary prediction for fungal biosynthetic gene clusters (BGCs), improved chemistry predictions for terpene, ribosomal peptide and non-ribosomal peptide BGCs, comparative alignment of trans-AT polyketide synthase (PKS) assembly lines and TTA codon annotation. A user interface was also introduced.
HPO / Human Phenotype Ontology
Provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO is developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. HPO also provides a large set of HPO annotations to approximately 4000 common diseases. HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things.
LINSIGHT
Provides a generalized linear model for functional genomic data and genome annotations. LINSIGHT is a computational method that outperforms state-of-the-art prediction methods in the task of prioritizing noncoding disease variants from the Human Gene Mutation database (HGMD) and the National Center for Biotechnology Information (NCBI) ClinVar database. By integrating a large number of genomic features, LINSIGHT provides a precise, high-resolution description of the fitness consequences of noncoding mutations in human genome.
Genewindow
Permits ‘genecentric’ annotation of the human genome for laboratory and analytical work carried out at the Core Genotyping Facility (CGF) of the National Cancer Institute. Genewindow integrates data available in the public databases with internal annotations from sequence data generated by our laboratory. It is configured for the human genome and can be applied to other genomes and integrated with the analysis, storage and archiving of data generated in any laboratory setting.
rVISTA
A comparative tool for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. rVISTA analysis proceeds in four main steps: (i) detect TFBS matches in each individual sequence using PWMs from the TRANSFAC database, (ii) identify pairs of locally aligned TFBSs, (iii) select TFBSs present in regions of high DNA conservation and (iv) create a graphical display that dynamically overlays individual or clustered TFBSs with the conservation profile of the genomic locus. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences.
MMseqs / Many-against-Many sequence searching
Allows clustering and searching of large protein datasets, such as UniProt, or 6-frame translated metagenomics sequencing reads. MMseqs is a software suite which contains three core modules: a pre-filtering module, an SSE2- and multi-core-parallelized local alignment module, and a clustering module. In addition to the modules, three workflows for sequence searching, clustering, and updating a clustering facilitate the most common tasks for the non-expert.
Pathway Tools
Allows management, analysis, simulation and visualization of integrated collections of genome, pathway and regulatory data. Pathway Tools is a bioinformatics software environment around a type of model-organism database called Pathway/Genome Database (PGDB). The software can manipulate genome data, metabolic networks and regulatory networks. For each datatype, it provides query, visualization, editing and analysis functions. It also provides visual tools for analysis of omics data sets, and tools for the analysis of biological networks.
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FlyBase
It is the leading website and database of Drosophila genes and genomes. FlyBase curates a variety of data from published biological literature, including phenotype, gene expression, interactions (genetic and physical), gene ontology (GO) information and many others. These data are organized in ∼31 different data-type reports such as the Gene Report or the Allele Report. The range of data we provide increases and changes as new types of data become available. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.
IGSR / International Genome Sample Resource
Expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups.
TCGA Data Portal / The Cancer Genome Atlas Data Portal
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Generates, analyzes, and makes available genomic sequence, expression, methylation, and copy number variation (CNV) data on over 11,000 individuals who represent over 30 different types of cancer. The information generated by TCGA is centrally managed and entered into databases as it becomes available, making the data rapidly accessible to the entire research community. TCGA is a collaborative effort led by the National Cancer Institute and the National Human Genome Research Institute to map the genomic and epigenomic changes that occur in types of human cancer, including nine rare tumors. Its goal is to support new discoveries through the generation of a catalog of somatic aberrations occurring in the different neoplasms, and accelerate the pace of research aimed at improving the diagnosis, treatment, and prevention of cancer.
International HapMap Project
A multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs.
OMIM / Online Mendelian Inheritance in Man
A comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. OMIM® is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. Genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (MIM numbers). OMIM® entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner.
EcoCyc
A scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc supports running and modifying E. coli metabolic models directly on the EcoCyc website.
COSMIC / Catalogue Of Somatic Mutations In Cancer
Enables to explore the impact of somatic mutations in human cancer. COSMIC is a database system that collects these somatic mutation data from a variety of public sources into one standardized repository, and make it easily explorable in a variety of graphical, tabulated and downloadable ways. The database encompasses all forms of human cancer. COSMIC is built primarily via curation of published literature by expert scientists. The database is also available for download in multiple formats.
EBI / EMBL-EBI - The European Bioinformatics Institute
Supplies an access to several biological data resources and bioinformatics services. EBI is a platform that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems, pathways, ontologies and literature. Databases, tools, as well as web services are provided for sharing data, performing queries and analyzing results. Users can also deposit their data through a data submission page. All the resources are freely available without restriction, with few exceptions.
JASPAR
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Offers a collection of extensively curated, non-redundant profiles collected from published collections of Transcription Factors Binding Sites (TFBS) from multicellular eukaryotes. JASPAR provides a web portal that provides a graphical interface for casual users, enabling browsing and database search functions, as well as basic sequence search functionality for selected profiles. It can also be used for seeking models for specific factors or structural classes, or if experimental evidence is paramount.
GXD / Gene eXpression Database
Offers an extensive and well-curated community resource of mouse developmental expression information. GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata.
REBASE
A comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. REBASE contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. From the REBASE website users have a variety of resources available that facilitate the analysis of sequence information, including tools for analyzing sequences (REBASE TOOLS), that allow restriction enzyme recognition sites to be found in submitted sequences (NEBCUTTER) and an implementation of BLAST to allow searching against all sequences in REBASE.
HGMD / Human Gene Mutation Database
Compiles information related to disease-related functional genetic variation in the germline. HGMD includes more than 200000 mutation entries, manually curated, obtained from the scientific literature. The database can be consulted in two formats: a public and a commercial version providing additional features. It can be used for supporting the pathological authenticity and/or novelty of detected gene lesions, establishing an overview of the mutational spectra for specific genes.
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