Bioinformatic Links

Below you'll find a list of some of my favorite bioinformatic links. It is nowhere close to comprehensive, but it allows me to keep a repository of links that I use and share. Hopefully you'll find them useful, also.

 

General Resources

Programming

  • R Studio - intuitive IDLE for the popular R script used in many open source scientific scripts
  • Python - simple language that is used in many scientific scripts
  • BioPython - great plugin containing modules for many scientific operations
  • Honorable mentions:

Bioinformatic Resources

  • NCBI - sponsored by the U.S. it contains favorites like BLAST and OMIM
  • EMBL/EBI - sponsored by the Europeans, it contains Ensembl, one of the most intutive and comprehensive gene analysis tools
  • ExPASy - sponsored by the Swiss, it contains some of the best protein structure analysis software including SWISS-MODEL
  • Broad - an MIT/Harvard collaboration which produces some of the advanced software, although it is not always user-friendly
  • Honorable mentions:

 

Reverse Genetics (Gene to Disease)

Genes

  • UCSC Genome Browser - classic premiere genome annotater which developed the horizontal track way of genetic annotation
  • Ensembl - from EMBL/EBI, it is a great resource for variant populations, comparative genomics and alternative splicing
  • BoSTON - a little self-serving, but this is my creation made in the Morton Lab, to apply proper nomenclature to rearrangements
  • Honorable mentions: BLAST, ClinVar, HGMI, Addgene,

Transcripts

  • GTEx - from Broad, it combines GWAS and RNASeq from human subjects to produce genome eQTL data
  • GEO - from NCBI, the Gene Expression Omnibus provides open source raw data from thousands of expression data sources
  • SHIELD - ear specific transcription data produced by my lab colleague Jun Shen, Ph.D.
  • Honorable mentions:

Proteins

  • Human Protein Atlas - relatively new, this group has developed a high-throughput antibody pipeline with tissue microarray validation
  • PDB - classic repository of protein crystal structures
  • SWISS-MODEL - very intuitive modeling program for tertiary structure
  • YASARA - a terrific GUI for protein modeling and simulation
  • Honorable mentions: Allen Brain Atlas, Prosite, Pfam

Pathways

  • KEGG - one of the best curated interactome databases and maps
  • GeneMANIA - although a little underpowered in studies, it has a great GUI for first time users
  • STRING - a popular protein-protein interaction webportal that always supplies structure information
  • GOrilla - is a GO enrichment tool to help analyze gene functional pathways
  • Honorable mentions: BioGRID

Models

  • ZFIN - bioinformatics from gene to phenotype in the zebrafish
  • Mouse Phenotype Portal - allows exploring several phenotypes that have been tested as part of KOMP
  • Honorable mentions:

 

Forward Genetics (Disease to Gene)

Disease and Phenotyping

  • OMIM - medical community favorite that describes Mendelian traits (NCBI has second OMIM portal)
  • HPO - Human Phenotype Ontology is a good standardized ontology applying a gene ontology model to phenotype
  • Honorable mentions:

Disease Gene Association

  • GWASdb2 - a NGO GWAS portal that supplies GWAS hits annotated on a horizontal track
  • DECIPHER - Sanger based repository of CNVs associated with diseases
  • cBioPortal - portal to The Cancer Genome Atlas which provides easily accessible mutation and transciptomic data on cancers
  • Hereditary Hearing Loss Homepage - repository of hearing specific Mendelian genes
  • Honorable mentions: