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Biological Sciences: Bioinformatics Resources

Bioinformatics Help

Please contact our Bioinformatics & Computational Biology librarian, Huajin Wang (huajinw@cmu.edu), for additional assistance with bioinformatics resources.

General Resources

NCBI (The National Center for Biotechnology Information): a centralized government-sponsored collection of resources for biomedical and genomic information, that includes databases, tools, tutorials, etc.

Help with NCBI ResourcesIn-person courses, live webinars and webinar recordings from NCBI

ExPASy - Bioinformatic Resource Portal: 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. 

Neuroscience

Allen Brain Atlas: a growing collection of resources integrating extensive gene expression and neuroanatomical data in mice, humans, and non-human primates. The data can be analyzed and viewed using a suite of portal tools (i.e. 3D viewer), as well as downloaded.

SFARI Gene: a curated database for autism research that contains interactive modules linking information about risk genes for autism with corresponding data from peer-reviewed research on human genes, animal models, and more

Genomics

ExAC Browser | The Exome Aggregation Consortium (ExAC): a dataset that spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies

HGMD - The Human Gene Mutation Database: a collated collection of published gene lesions responsible for human inherited disease

UCSC Genome Browser: a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data

GWAS Cataloga quality controlled, manually curated, literature-derived collection of all published genome-wide association studies assaying at least 100,000 SNPs and all SNP-trait associations with p-values < 1.0 x 10-5. Also publishes the iconic GWAS diagram of all SNP-trait associations, with p-values ≤ 5.0 x 10-8, mapped onto the human genome by chromosomal locations and displayed on the human karyotype.

SGD - Saccharomyces Genome Databaseprovides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms

FlyBase: a database for Drosophila genes and genomes 

Protein Secondary Structure Prediction

ExPASy - ProtScale: a tool that allows you to compute and represent the profile produced by any amino acid scale on a selected protein

UniProta comprehensive and high-quality resource of protein sequence and functional information

HeliQuest: an excellent tool for predicting helices from amino acid primary sequence 

TOPCONS: consensus prediction of membrane protein topology and signal peptides

TMMOD: Hidden Markov Model for Transmembrane Protein Topology Prediction 

Pathway Analysis

BiNGO: a Java-based tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network

KEGG: a collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases, and drug development

PANTHER: a classification system of proteins (and their genes) in order to facilitate high-throughput analysis

Gorilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool): Identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).

DAVID Bioinformatics Resources:  a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes

Disease-Specific

canSAR: a tool to enable cancer translational research and drug discovery that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions

SFARI Gene: a curated database for autism research that contains interactive modules linking information about risk genes for autism with corresponding data from peer-reviewed research on human genes, animal models, and more

Biological Sciences, Biomedical Engineering, and Neuroscience Librarian

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Melanie Gainey
Contact:
Mellon Library
4th Floor Mellon Institute
412-268-3171