Simen Lab Resources

Bioinformatics

General sequence related information

• 123 Genomics -- Everything relevant to bioinformatics
• Atlas Web Tools -- Retrieve sequences using various types of information
• BLAST -- Molecular search
• Ensembl -- Various genomic resources
• GeneCards -- Comprehensive information on genes
• Gene-Entrez -- Gene-level information
• Harvester-EMBL -- Various information on genes
• Human genome BLAST
• NCBI -- Integrated biological data
• PubGene -- Comprehensive bioinformatics resources
• PubMed Assistant
• Rat Genome Database
• UCSC-Home -- Various genomic resources
• UniGene -- Homology & where expressed & chromosome location & ESTs

Alignments

• Lagan -- Stanford sequence aligner for big genomic DNA
• Multi-ALign -- Multiple Sequence Alignments
• SIM4 -- Alignment of cDNA and genomic DNA
• SPIDEY -- Alignment of cDNA and genomic DNA

Annotation

• AmiGO Browser -- Find GO IDs for specific GO terms
• DAVID -- Gene annotation and functional over-representation analysis
• GALAXY -- Annotation across species and more
• Genmapp -- Analysis of expression data in context of pathways and GO terns
• Geneontology.org Tools -- List of many annotation tools
• GEPAS -- Gene Expression Pattern Analysis
• GO -- Gene Ontology Tools
• gpDB -- Database of GPCRs
• Housekeeping Genes -- List of housekeeping genes with accession numbers
• MatchMiner -- Convert between various sequence identifiers
• MGI -- Mouse genome informatics (Jax)
• Onto-Express Pathway Express -- Tools for mapping
• Ontology Traverser -- Web and R tool for GO analysis
• RegRNA -- RNA regulatory sites finder (iincludes 5' and 3" UTRs)
• SeqExpress - Package for secondary analysis and display
• SOURCE -- Gene ID interconversion
• Tree Machine
• Tiger Steroid Hermone Site Finder
• Treemap -- Software for hierarchical data display
  

Array CGH

• DNAcopy package
• GLAD package
• SNAP package

Arrays

• Affymetrix -- home page
• Array Software Comparison
• Keck Affymetrix Gene Chip Resource Center
• Eisen Lab Array Software (Clustering)
• Microarray Power Atlas
• Yale Keck Microarrays (not Affymetrix)
• Yale Keck Biostatistics
• Yale Microarray Database

Brain Anatomy and Expression

• Allen Brain Atlas -- 3D mouse gene expression atlas
• Brain gross anatomy - Human
• Brain surface anatomy - Human
• Gensat -- Expression Data

ESEs (Exon splice enhancers)

• ESEfinder -- CSHL exon splice enhancer search
• SeeEse -- TIGR exon splice enhancer search

Evolution

• C.elegans project - Wormpep
• ECR Browser -- Comparative genomics browser (dCODE)
• GALA -- Multiple species alignment and conservation information
• VISTA -- Enhancer and conserved non-coding browser
  

Genetic Mapping Software

• Abecasis -- Homepage to access Merlin, QTDT, etc.
• eHap -- Haplotype association analysis (U. Pitt)
• FBAT & PBAT -- Family based association analysis
• Genetic Power Calculator -- Simple power calculations for genetics
• Haplopainter -- Pedigree drawing software download (JAVA)
• Haploview -- SNP selection & LD blocks & analysis
• Linkage format -- Users guide to the Linkage file format
• Paw3D -- Power analysis software for association studies (Download)
• PBAT -- Christoph Lange's PBAT site
• Pittsburgh Genetics Software -- Access to Mega2 SLINK Simwalk2 etc.
• Pritchard -- Jonathan Pritchard's software (e.g. STRUCTURE)
• Quanto -- Genetic power analysis (G, E, GxE, quant. and qual) from USC
• Rockefeller Linkage Software -- Links to just about everything
• SAGE -- Genetic analysis package
• SNPSpD -- SNP spectral decomposition to estimate # independent tests
• WebQTL -- Oak Ridge Labs web based QTL mapping resource

Imaging

• Fluorescent spectra comparison tool

IRES sequences

• IRES database

Methylation

• BiSearch -- Bisulfite sequencing primer design
• MethPrimer -- Methylation PCR design for bisulfite sequencing

miRNA (Micro RNAs)

• MicroInspector -- miRNA binding prediction

Mouse anatomy

• Jax Mouse Anatomy

NESs (Nuclear export signals)

• NESbase -- Nuclear Export Signal Prediction

Pathways

• Biocarta -- Pathways
• KEGG -- Pathways

Primer Design

• PCR Suite -- Improved Primer3-based primer design including design of multiple overlapping primers
• Primer Bank -- Human and Mouse Q-PCR Primers
• Primer3 -- Primer design

Promoters and Transcription Factors

• FirstEF -- Promoter and first exon prediction program
• OTFBS -- Over-represented transcription factor binding
• PrimerStation -- Multiplex primer design for the Human genome
• PROMOSER -- Promoter sequence extraction
• SIB-EPD -- Promoter Database
• TESS - Transcription factor search
• TFSEARCH -- Search for transcription factor binding sites in a promoter
• TRANSFAC -- Transcription factor binding database
• VISTA -- Enhancer and conserved non-coding browser

Proteomics

• ExPASy -- Various proteomics tools

Variation in the genome including disease genes and markers

• ALFRED -- Kidd lab allele frequency database
• dbSNP -- NCBI SNP Database
• Genetic association database
• Hapmap -- Home page to the Hapmap project
• HGMD -- Human Gene Mutation Database -
• Comprehensive mutation information
• Medgene -- Disease-Gene association database
• OMIM -- Online Mendelian Inheritence in Man
• SNP Cutter

Ethics and Funding

• Burroughs Wellcome Fund
• Campus Partners
• Congressionally Directed Medical Research Programs eReceipt
• COS Funding Alerts
• CRISP -- Searchable database of current grants
• Foreign funding opportunities
• GrantsNet -- Searchable grant database
• ICMJE authorship guidelines
• NARSAD foundation
• NIH Commons Grant site -- Information on your grants
• NIH Extramural Grants
• NIH Loan repayement programs
• NIH PHS 398 forms and instructions
• Sallie Mae
• Stanley Foundation
• Yale Grants Page
  

Programming and other open soure software

• Active State PERL
• ActiveState Python -- Python programming for Windows
• Animal behavior software links
• Bioconductor -- R tools for bioinformatics
• BioEdit -- Nice sequence manipulation program
• Bioinformatics.org -- Open Source Bioinformatics software
• BioPERL Site
• Bloodshed Dev C++ Open Source Compiler
• BUGS software -- Bayesian inference Using Gibbs Sampling
• CPAN -- PERL resource site
• CRAN -- Resource site for the R package
• Crimson Editor -- Nice source code editor
• CSPro -- Census and Survey Processing System
• EditPad Lite -- Source code editor, can handle any number of characters per line
• EMBOSS -- High quality open source bioinformatics package
• EthoLog -- Behavior software
• FTLK Fast Light Toolkit for GUIs in C/C++
• GeneDoc -- Sequence alignmnet shading software
• Genographer -- Open source fragment analysis software
• GGobi -- Data visualization system for viewing high-dimensional data
• JWatcher -- Animal behavior scoring software
• NIH Image J -- Excellent image analysis software for microscopy and gels
• Notepade++ -- Nice open-source source code editor
• Open-PERL IDE -- Open source development environment/editor for PERL programming
• PEBL -- The Psychology Experiment Building Language
• PERL2Exe -- Generate executable code from PERL scripts
• Python programming for bioinformatics -- online course
• Scigraphica -- Open Source version of Origin for Linux only
• SEE Workship -- Behavioral analysis from XY coordinate data
• Sourceforge -- Open Source repository
• STRAND -- Open source fragment analysis software
• Tinn-R -- Open source environment/editor for R programming
• Winbugs -- Bayesian inference Using Gibbs Sampling
• Zeiss Axiovision image viewer
  

Vendors

ABgene  -  Affymetrix  -  Ambion  -  Amersham  -  ABI  -  ATCC
BD  -  Bio-Rad   -  Braintree Scientific  -  Cell Sciences  -  Chemicon  -  Fisher - IDT  -  Invitrogen  -  JAX  -  Labsource
Mathworks  -  Multivariate Software -   NEB  -  Newegg  -  Promega  -  QBiogene -  Qiagen   -  R&D Systems  -  Roche
SAS  -  Sigma-Aldrich  -  Softgenetics  -  Stem Cell Tech   -  Stratagene -  USA Scientific  -  Wolfram  -  Yale-DNA

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