Tools

General

Database Description

Help

CBS Prediction Servers

A list of sequence prediction tools provided by CBS.

 

EBI-EMBL Tools A list of popular, free bioinformatic software generated by EBI-EMBL.  
ExPASy ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.  
Galaxy Galaxy is an open source, web-based platform for data intensive biomedical research, including NGS sequence analysis, ChIPSeq Analysis and SNP/indel identification. It's a great "gateway" to using commandline tools. 

Galaxy 101

Videos
 

Wiki

Genome Space GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. Support
NCBI Analyze NCBI provides a wide variety of data analysis tools that allow users to manipulate, align, visualize and evaluate biological data.  

Sequence Alignment

Database Description

Help

BLAST The Basic Local Alignment Search Tool (BLAST) finds regions of homology between your query and a chosen search set (database). This site contains various algorithms for protein and nucleotide sequences.

Help

ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences.  
EBI EMBL Multiple Sequence Alignment Multiple Sequence Alignment (MSA) is generally the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied.  
EBI-EMBL Pairwise Sequence Alignment Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).  
EMBOSS Water EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancements) to calculate the local alignment of two sequences. Help

Protein Structure and Function

Database Description

Help

CDART The Conserved Domain Architecture Retrieval Tool (CDART) performs similarity searches of the Entrez Protein database based on domain architecture, defined as the sequential order of conserved domains in protein queries. CDART finds protein similarities across significant evolutionary distances using sensitive domain profiles rather than direct sequence similarity. Help
Phobius Phobius is a program for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. Help
EMBL-EBI Protein Functional Analysis A compilation of protein analysis tools provided by EBI-EMBL  
PfamScan PfamScan allows the user to search a FASTA sequence against a library of protein families with known function. Help
SignalP SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Instructions
VAST Vector Alignment Search Tool (VAST) is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures ("similar structures") by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Help

Cancer Genomics

Database Description

Help

Broad GDAC Firehose Provides systematic pipelines for analyzing data from the Cancer Genome Atlas (TCGA). This resource includes versioning of datasets, analysis results, biologist friendly reports, and custom runs.

 

Gene Spot This tool provides a way to view TCGA data from a gene-centric point-of-view. It includes a number of interactive visualizations, and allows the user to save their current exploration. This application also enables the user to select specific tumor types and genes of interest, and load data that is generated from a variety of TCGA analysis.  
IGV Integrated Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

User's Guide

FAQ

InSilico InSilico DB aggregates more than 250,000 samples of microarray and RNA–Seq data (human, mouse and rat) coming from public repositories including GEO and TCGA.  
Regulome Explorer Regulome Explorer facilitates the integrative exploration of associations in clinical and molecular TCGA data. Regulome Explorer is an effort by the Center for Systems Analysis of the Cancer Regulome (CSACR), a collaboration between the Institute for Systems Biology and The University of Texas MD Anderson Cancer Center. CSACR is a Genome Data Analysis Center within The Cancer Genome Atlas project.

User Guide

Quick Start Guide

 

TCGA Batch Effects Tool This website is designed to help assess, diagnose and correct for any batch effects in TCGA data. It first allows the user to assess and quantify the presence of any batch effects via algorithms such as Hierarchical Clustering and Principal Component Analysis. The results from these algorithms are presented graphically as both simple and interactive diagrams. If significant batch effects is observed in the data, the user then has the option of downloading data that has been computationally corrected using methods such as Empirical Bayes (aka. ComBat), Median Polish and ANOVA.  

Genetic Variation

Database Description

Help

NCBI variation tools Main page for all NCBI variation tools. 

 

Variation Reporter

NCBI Variation Reporter is a tool for accessing the content of human variation resources at NCBI.  You may query our data using your variant calls in a variety of formats.  We will match them to our data to produce a report that draws on dbSNP, dbVar, ClinVar, and NCBI's own human genomic annotation.

Help

FAQ

Examples

Variation Viewer Variation Viewer is a tool for interactive examination and download of nucleotide variants for a specific locus.  It supports both the GRCh38 and GRCh37.p13 assemblies.  Variation Viewer integrates data from all of the NCBI Variation databases and presents them in a coupled graphical and tabular report.  The resulting list of variants can be saved locally using the download function.  You can also upload their own variant data to this browser. 

 

Introductory Video tutorial

1000 Genomes Browser 1000 Genomes Browser allows you to review sequence alignments and variant calls from the 1000 Genomes Project in the context of various genome annotations.  Browse data by population or individual sample, as well as by sequencing platform, aligner or experiment type.  Download genome slices of sequence and alignment data or genotype calls.  Users can also upload their own data into the browser.  All data is displayed in GRCh37.p13 coordinates.

Help

FAQ

NCBI Genome Remapping Service The NCBI Genome Remapping Service is a tool that projects users' annotation data from one coordinate system to another.  With the Assembly-Assembly remap, you can remap your variant calls between different assembly versions, while the Clinical Remap permits you to remap data between RefSeqGenes or LRGs and an assembly, using NCBI calculated alignments.  
PheGenI The Phenotype-Genotype Integrator is a tool that integrates the search and retrieval of associated genotype-phenotype data from National Human Genome Research Institute (NHGRI) Genome-wide Association Study (GWAS) Catalog integrated with data housed in Gene, dbGaP, OMIM, GTEx and dbSNP.   It provides search by genotype and phenotype.  The dbSNP Data in NCBI PheGenI is only mapped GRCh38 at this time.  

Immunology Tools

Database Description

Help

SPS EpiToolKit SBS EpiToolKit is a service of the Division for Simulation of Biological Systems at University of Tübingen. The aim of this website and its services is to support immunological research. It provides a collection of methods from computational immunology for the prediction of MHC ligands or potential T-Cell epitopes.  
NetMHC 3.4 Server Predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs).  
PIGS PredictioPigs is a web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion. Its final output is a complete three-dimensional model of the target antibody that can be downloaded or displayed on-line. The server is freely accessible to academic users, with no restriction on the number of submitted sequences.