Informatics Resources Available to NEI Researchers

Nucleic Acid focused tools

• Promoter Analysis
  • Promoter and transcript prediction

    Name:	New GENSCAN Web Server at MIT
    Description:	Reports positions of predicted features in tab-delimited form.
    Source:	http://genes.mit.edu/GENSCAN.html
    Coments:	Very fast and easy. Processes up to 1 million base pairs of sequence.

    Name:	GrailEXP
    Description:	Desktop software for finding positions of promoter elements
    Source:	http://compbio.ornl.gov/Grail-1.3/
    Coments:	Down load and install the program; runs locally.

  • Retrieve DNA sequences for predicted promoter regions

    Name:	PromoSer
    Description:	Using GenBank Accession IDs, PromoSer returns FASTA-formatted promoter region sequence.
    Source:	http://biowulf.bu.edu/zlab/PromoSer/
    Coments:	Only available species are human, mouse and rat.

    Name:	EPD: The Eukaryotic Promoter Database
    Description:	Retrieves DNA sequence and/or annotations for a large selection of species. Query by Accession ID or text description.
    Source:	http://www.epd.isb-sib.ch/
    Coments:	A great deal of useful information beyond DNA sequence is available. Rather slow.

  • Identify predicted transcription factor binding-sites in a DNA sequence

    Name:	TFSEARCH
    Description:	Annotates input DNA sequence with transcription factor binding-sites, displaying factor names and matrix-match score statistics in the same view.
    Source:	http://www.cbrc.jp/research/db/TFSEARCH.html
    Coments:	Easy and fast but display format is difficult to use.

    Name:	TESS - Transcription Element Search System
    Description:	Searches DNA sequences for transcription factor binding-sites using TransFac.
    Source:	http://www.cbil.upenn.edu/cgi-bin/tess/tess
    Coments:	Easy to use. Numerous options for graphical or tabular output display and download.

    Name:	WWW Promoter Scan
    Description:	Predicts probability and location of promoters in input sequence. Reports transcription factor binding-sites.
    Source:	http://www-bimas.cit.nih.gov/molbio/proscan/
    Coments:	Criteria for transcription factor binding-sites are stringent.

    Name:	BioProspector
    Description:	Examines the upstream region of a group of genes for shared sequence motifs.
    Source:	http://robotics.stanford.edu/~xsliu/BioProspector/
    Coments:	Select Motif Finding to access the on-line version. This is useful for comparing promoters of co-coordinately regulated genes (i.e. microarray results), with user defined search parameters. Since transcription factor databases are not used, novel conserved motifs may come to light.

    Name:	CompareProspector
    Description:	This extends BioProspector by including orthologs.
    Source:	http://compareprospector.stanford.edu/index.html
    Coments:	Select Search to begin. User must provide sequence alignments of orthologs.

    Name:	Genomatix
    Description:	Scan sequences for single transcription factor binding-sites or for ‘modules’; design promoter models from co-occurrence of patterns of binding-sites in coordinately regulated genes.
    Source:	http://www.genomatix.de/
    Coments:	See Dr. Cynthia Jaworski (Jaworski@helix.nih.gov) who holds the individual license.

    
    
  • CpG Island Detection

    Name:	CpGPlot/CpGReport/Isochore
    Description:	Produces graphical as well as text reports of CpG content.
    Source:	http://www.ebi.ac.uk/emboss/cpgplot
    Coments:	Numerous options available for customizing your search.

    Name:	CpGProD
    Description:	Scans multiple sequences for CpG islands.
    Source:	http://pbil.univ-lyon1.fr/software/cpgprod_query.php
    Coments:	Limited options but simple to use.

    
    
• Primer design
  • MolBio-tools for PCR

    Name:	MolBio-tools for PCR
    Description:	Portal to web-based software for PCR applications.
    Source:	http://molbiol-tools.ca/PCR.htm
    Coments:	From simple to extremely complicated design parameters. siRNA design.

  • NCBI: primer-blast

    Name:	NCBI: primer-blast
    Description:	Combines a BLAST search with PCR primer design to ensure specificity.
    Source:	http://www.ncbi.nlm.nih.gov/tools/primer-blast/
    Coments:	A new offering from NCBI in 2008.

  • Primer3

    Name:	Primer3
    Description:	Design PCR primers or hybridization probes.
    Source:	http://biotools.umassmed.edu/bioapps/primer3_www.cgi
    Coments:	Very popular.

• RNA Resources
  • RNA

    Name:	The RNA World Website
    Description:	Provides tutorials on RNA related topics and links to web tools and databases of various types of RNA and RNA structures.
    Source:	http://www.imb-jena.de/RNA.html
    Coments:	A comprehensive resource.

  • microRNA

    Name:	miRBase::Sequences (SANGER)
    Description:	Database of miRNA sequences and nomenclature, a registry facility for adding miRNAs to the database, and tools for target prediction.
    Source:	http://microrna.sanger.ac.uk/sequences/
    Coments:	The most comprehensive resource for miRNA

    Name:	TargetScan 4.0
    Description:	Query by Entrez Gene symbol or microRNA name to return target-site matches within UTRs.
    Source:	http://www.targetscan.org/vert_40
    Coments:	Considered by many to be the best target prediction resource. The UCSC genome browser has an annotation track using TargetScan predictions.

    Name:	The RNAi Web
    Description:	Provides tutorials about siRNA and miRNA; links to programs on other websites.
    Source:	http://www.rnaiweb.com/
    Coments:	Emphasis on siRNA.

    Name:	MiRanda
    Description:	microRNA.org: A resource for predicted microRNA targets and expression data.
    Source:	http://www.microrna.org/
    Coments:	Extensive expression database.

    Name:	miRGator
    Description:	Predicts miRNA binding-sites, starting from either the transcript ID or the microRNA ID. Databases of the tissue distribution of miRNA and miRNA-enriched pathways.
    Source:	http://genome.ewha.ac.kr/miRGator/miRGator.html
    Coments:	Perform simultaneous target prediction with 3 different algorithms.

    Name:	miRDB
    Description:	Predicts microRNA binding-sites, starting from either the transcript ID or the microRNA ID. Explore hypothesized regulatory networks using lists of genes or miRNAs.
    Source:	http://mirdb.org/miRDB/
    Coments:	Links to Panther and to a Wiki annotation page.

    Name:	MiRAlign
    Description:	Predicts target-sites for miRNA binding from raw input sequence.
    Source:	http://bioinfo.au.tsinghua.edu.cn/miralign/
    Coments:	Fast.

Useful for both Nucleic Acid and Protein analyses

• Assembling and managing sequence data
  • Sequencher

    Name:	Sequencher
    Description:	Software for assembling sequence project data into contigs. Tools for sequence analysis and annotation.
    Source:	NEI license: http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Comment:	Rapid assembly of contigs, visual tools for examining chromatographs. Intuitive, easy to use.

  • DNAStar/Lasergene

    Name:	DNAStar (Lasergene)
    Description:	A suite of individual programs using a common sequence file format. Use for contig assembly, viewing DNA sequence chromatographs, multiple sequence alignment, protein structure analysis and prediction, primer design, and more.
    Source:	NEI license: http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Comment:	Very functional. Rapid assembly of contigs, visual tools for examining chromatographs. Intuitive, easy to use.

• Alternative BLAST servers (if NCBI is down)
  • BLAST at GenomeNet

    Name:	BLAST at GenomeNet
    Description:	Kyoto University Bioinformatics Center
    Source:	http://blast.genome.jp/
    Coments:	All varieties of BLAST are run from the same web page.

  • BLAST at EMBnet

    Name:	BioEdit
    Description:	Swiss Institute of Bioinformatics
    Source:	http://www.ch.embnet.org/software/aBLAST.html
    Coments:	All varieties of BLAST are run from the same web page.

• Multiple Sequences: Align and Edit
  • BioEdit

    Name:	BioEdit
    Description:	A menu-driven program for aligning or editing alignments.
    Source:	Download from http://www.mbio.ncsu.edu/BioEdit/BioEdit.html
    Coments:	Excellent choice for publication quality figures because of the many display options.

  • MegAlign

    Name:	MegAlign
    Description:	One of the programs in the DNAStar/LaserGene Suite.
    Source:	NEI license http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Coments:	It works well and interfaces seamlessly with EditSeq. Edit options not very intuitive.

Protein, Lipid Analysis focused tools

• Protein Sequence Analysis
  • Scan protein sequences for functional motifs and potential sites for post-translational modifications

    Name:	ExPASy - PROSITE
    Description:	Search for protein domains, families and functional sites from the Prosite database. Scan individual protein sequences or find domains common to multiple sequences. Graphical output shown in cartoon format.
    Source:	http://ca.expasy.org/prosite/
    Coments:	Produce your own domain figures with the "MyDomains-Image Creater" drawing tool.

    Name:	SIB - Swiss Institute of Bioinformatics
    Description:	Input sequences are scanned for motifs from Prosite, Pfam, and InterPro databases.
    Source:	http://hits.isb-sib.ch/cgi-bin/PFSCAN
    Coments:	Aligns your sequence with a canonical sequence or motif. Test sequences are provided to support a fast learning-curve for each tool.

    Name:	SMART: Simple Modular Architecture Research Tool
    Description:	Scan for domains from SMART and PFAM databases and identify internal repeats and signal peptides in the Sequence Analysis section.
    Source:	http://smart.embl-heidelberg.de/
    Coments:	The Architecture Section is a useful adjunct to the sequence analysis. It identifies proteins sharing conserved combinations of domains.

    Name:	MOTIF Search
    Description:	Scan a protein sequence for motifs from PROSITE, BLOCKS, ProDom, PRINTS, Pfam, or user-defined database.
    Source:	http://motif.genome.jp/
    Coments:	Avoid selecting all databases at once or the server connection may time-out.

    Name:	SCOP: Structural Classification of Proteins
    Description:	A database of structural and evolutionary relationships between proteins whose structures are known.
    Source:	http://scop.mrc-lmb.cam.ac.uk/scop/
    Coments:	A resource for putting your protein of interest in context.

    Name:	CBS Prediction Servers
    Description:	Detect sites of post-translational modifications, protein sorting signals, immunological features, and perform a number of functional and structural predictions.
    Source:	http://www.cbs.dtu.dk/services/
    Coments:	Well documented explanations of output.

    Name:	NPS@: Network Protein Sequence Analysis.
    Description:	Detects features from the PATTINPROT, PROSCAN and InterProScan databases.
    Source:	http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html
    Coments:	The site also offers a variety of other useful tools that defy classification.

    Name:	Protein Data Bank
    Description:	An Information Portal to Biological Macromolecular Structures.
    Source:	http://www.rcsb.org/pdb/home/home.do
    Coments:	The major resource for known protein structures.

    
    
  • Protein-protein Interactions

    Name:	IntAct
    Description:	Open source database system and analysis tools for protein interaction data.
    Source:	http://www.ebi.ac.uk/intact/site/index.jsf
    Coments:	Appears to be the most up-to-date database for interaction data.

    Name:	The BioGRID
    Description:	The General Repository for Interaction Datasets, database of physical and genetic interactions for model organisms.
    Source:	http://www.thebiogrid.org/
    Coments:	Easy to use. Linked to OSPREY (http://biodata.mshri.on.ca/osprey/servlet/Index), an online tool for visualizing your own networks and expanding them using GO term associations.

    Name:	MINT: Molecular INTeraction database
    Description:	A manually curated collection of experimentally verified protein-protein interactions
    Source:	http://mint.bio.uniroma2.it/mint/Welcome.do
    Coments:	Results returned as text, or can be converted to an interactive graphical view of the connected proteins. The graphical view can be used as a pathway builder.

    Name:	Networks: portal for networks research in the Gerstein Lab
    Description:	Tools for visualizing your own interaction data.
    Source:	http://networks.gersteinlab.org/
    Coments:	tYNA is the “primary” networks software available on this site.

  • Subcellular protein localization

    Name:	PSORT WWW Server
    Description:	Scans input peptide sequence for motifs that target proteins to organelles or particular regions within a cell. Output indicates presence or absence of motifs with statistical scoring.
    Source:	http://psort.ims.u-tokyo.ac.jp/
    Coments:	Quick and potentially very useful.

• Lipid Resources
  • LIPID BANK for Web

    Name:	LIPID BANK for Web
    Description:	Database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
    Source:	http://lipidbank.jp/
    Coments:	Provides structures, nomenclature, references, and chemical information data.

Systems Biology tools

• GENE ID Conversion
  • Convert gene ID formats, and add functional annotations such as GO terms or KEGG pathways.

    Name:	Clone|Gene ID Converter
    Description:	Annotate lists of gene names, GenBank accession numbers, or IDs for Entrez, Unigene, RefSeq, Affymetrix IDs. Output options include functional, clone, protein, genome location, and gene level information.
    Source:	http://idconverter.bioinfo.cnio.es/
    Coments:	Very versatile. Output downloads as an Excel file. Only available for human, mouse, and rat.

    Name:	DRAGON Database
    Description:	Find Entrez Gene, Unigene IDs, and other annotations for GenBank accession numbers.
    Source:	http://pevsnerlab.kennedykrieger.org/annotate.htm
    Coments:	Only available for human, mouse, and rat.

    Name:	G:Profiler
    Description:	Finds microarray probes according to specific commercial arrays. Nomenclature identifiers also available for output.
    Source:	http://biit.cs.ut.ee/gprofiler/gconvert.cgi
    Coments:	Handles 39 species.

• Gene Expression Databases
  • NEIBank

    Name:	NEIBank
    Description:	Genomics and bioinformatics databases/resources for vision research.
    Source:	http://neibank.nei.nih.gov/index.shtml
    Coments:	Our favorite!

  • Mouse genome informatics

    Name:	Mouse genome informatics
    Description:	Database resource for the laboratory mouse: allelic variants correlated with phenotypes.
    Source:	http://www.informatics.jax.org/
    Coments:	Excellent integration of genomic and phenotypic data.

• Gene Ontology and Annotation
  • Gene Ontology

    Name:	The Gene Ontology Home
    Description:	Search for GO annotations or browse the ontology.
    Source:	http://www.geneontology.org/
    Coments:	This is the homepage of the consortium that organizes GO assignments.

    Name:	GO-SCAN Online: Gene Ontology Significant Collection of Annotations
    Description:	Examine Affymetrix microarray results.
    Source:	http://goscan.cit.nih.gov/
    Coments:	Accepts limited repertoire of chips, but simple to use. Developed by CIT.

    Name:	GoMiner
    Description:	Process microarray data with many options for parameters and output content.
    Source:	http://discover.nci.nih.gov/gominer/
    Coments:	Desktop or web interface, developed by NCI.

  • Annotation Analysis

    Name:	DAVID: Database for Annotation, Visualization and Integrated Discovery
    Description:	Functional annotation tools. Tools for detecting over-representation of functional categories in gene sets.
    Source:	http://niaid.abcc.ncifcrf.gov/
    Coments:	Developed by NIAID, NIH. An industry ‘standard’.

    Name:	Panther: Protein ANalysis THrough Evolutionary Relationships
    Description:	Single genes or lists of genes can be categorized according to molecular function.
    Source:	http://www.pantherdb.org/
    Coments:	Output associates your queries with pathways.

  • Comparing Gene Lists

    Name:	Babelomics
    Description:	Examine lists for gene set enrichment, GO annotation; perform ID conversion.
    Source:	http://www.babelomics.org/
    Coments:	Similar to DAVID, but organized differently.

    Name:	WebGestalt: Web-based Gene Set Analysis Toolkit
    Description:	Compare contents of 2 lists of genes using Boolean operators.
    Source:	http://bioinfo.vanderbilt.edu/webgestalt/index.php
    Coments:	Quick and simple. Output associates your queries with pathways.

    Name:	GSEA: Gene Set Enrichment Analysis
    Description:	Client server software for determining whether an a priori defined set of genes is similar to any other similarly defined set of genes.
    Source:	http://www.broad.mit.edu/gsea/index.jsp
    Coments:	The tutorials and documentation are excellent. Also, CIT regularly offers GSEA-training. Output associates your queries with pathways.

    Name:	CMAP: Connectivity map
    Description:	Archive of drug and small molecule effects upon gene expression in cultured cells. Compare your microarray results for similar trends.
    Source:	http://www.broad.mit.edu/cmap/
    Coments:	Facilitates "discovery of functional connections between drugs, genes and diseases."

• Pathways
  • KEGG

    Name:	KEGG (Kyoto Encyclopedia of Genes and Genomes)
    Description:	Maps representing molecular interactions and reaction pathways.
    Source:	http://www.genome.jp/kegg/
    Coments:	A standard archive of pathway information.

  • Ingenuity Pathway Analysis

    Name:	Ingenuity Pathway Analysis (IPA)
    Description:	Using IPA developed ontology, classifies gene lists for functions and associations with known pathways and de novo created networks.
    Source:	NIH license through the NIH library. Contact Doug Joubert. joubertd@ors.od.nih.gov
    Coments:	Dr. Katherine Peterson (PetersonK@nei.nih.gov) is a certified specialist for this application and is available to assist users.

  • Explain

    Name:	Explain
    Description:	Part of Biobase suite of programs; for matching microarray results with canonical pathways.
    Source:	http://helixweb.nih.gov/biobase/index.html
    Coments:	Available from CIT, with access via NIH login and password.

  • Genomatix

    Name:	Genomatix
    Description:	Pathway analysis with emphasis on upstream transcription factors.
    Source:	http://www.genomatix.de/
    Coments:	See Dr. Cynthia Jaworski (Jaworski@helix.nih.gov) who holds individual license.

  • Pathway Studio

    Name:	Pathway Studio
    Description:	Explore relationships among genes based upon a database of molecular associations produced by "natural language processing" technology, drawn from the entire PubMed.
    Source:	http://www.ariadnegenomics.com/
    Coments:	See Dr. Cynthia Jaworski (Jaworski@helix.nih.gov) who holds individual license.

General Bioinformatics tools

• Phylogeny
  • Phylogeny Programs

    Name:	Phylogeny Programs
    Description:	Portal to software for inferring phylogenies (evolutionary trees). The list can be sorted by various criteria, such as computational method or platform.
    Source:	http://evolution.genetics.washington.edu/phylip/software.html#methods
    Coments:	An interesting way to interface with the molecular evolution community.

  • MEGA - Molecular Evolutionary Genetics Analysis

    Name:	MEGA - Molecular Evolutionary Genetics Analysis
    Description:	Offers a variety of tree-building methods for protein and nucleotide sequences. Import sequence alignments or use the MEGA alignment editor.
    Source:	Download from: http://www.megasoftware.net/
    Coments:	Favorite from the above list. Includes an excellent tutorial explaining the methods and navigating the program.

• Literature Mining
  • QUOSA

    Name:	QUOSA
    Description:	Retrieves and archives full text articles and provides alerting services.
    Source:	NEI license.http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Coments:	Tutorials by the makers of QUOSA are excellent. CIT and/or the NIH library sponsor these frequently.

  • IHOP (Information Hyperlinked Over Proteins)

    Name:	IHOP (Information Hyperlinked Over Proteins)
    Description:	Search tool for retrieving summaries of information about query terms using networks established by the association of terms in the scientific literature.
    Source:	http://www.ihop-net.org/UniPub/iHOP/
    Coments:	Using IHOP is truly intuitive. Information can be directly incorporated into a visual "Gene Model" of connected proteins.

  • ZOTERO

    Name:	ZOTERO
    Description:	A tool for organizing and saving web-based research. Captures and stores PDFs, images, web pages; items can be custom–tagged and annotated.
    Source:	Free download from http://www.zotero.org/
    Coments:	Requires Firefox as the internet browser. This is fabulous.

• Portals: Multi-functional websites and lists of links
  • BioCluster

    Name:	BioCluster
    Description:	NIAID Bioinformatics Portal
    Source:	https://niaid-biocluster.niaid.nih.gov/cgi-bin/bipod2/index.cgi
    Coments:	Register to gain access using your NIH USER ID and password. NIAID has a large and active bioinformatics group supporting the software on this site and providing training through CIT.

  • Mobyle, a portal for bioinformatics analyses

    Name:	Mobyle, a portal for bioinformatics analyses
    Description:	A portal for database searches, sequence pattern analysis, phylogeny, and structure tools.
    Source:	http://bioweb2.pasteur.fr/intro-en.html
    Coments:	A broad range of resources.

  • European Bioinformatics Institute

    Name:	European Bioinformatics Institute
    Description:	A directory of molecular biology links.
    Source:	http://www.ebi.ac.uk/services/
    Coments:	A broad range of resources

  • Online Analysis Tools

    Name:	Online Analysis Tools
    Description:	Portal for tutorials, carbohydrate analysis, sequence analysis, and miscellaneous tools for calculations at the bench.
    Source:	http://molbiol-tools.ca/
    Coments:	Excellent. From the Department of Microbiology & Immunology, Queen's University, Ontario, Canada. Check out the Electrophoresis simulation in the tutorials section.

  • EMBnet

    Name:	EMBnet
    Description:	Portal to BLAST gateways, alignment programs, and sequence analysis tools.
    Source:	http://www.ch.embnet.org/index.html/
    Coments:	Some items are unique. Hosted by the Swiss Institute of Bioinformatics.

  • Bioinformatics World Alphabetical List

    Name:	Bioinformatics World Alphabetical List
    Description:	Alphabetical directory portal of databases and tools.
    Source:	http://homepage.univie.ac.at/herbert.mayer/AtoZ.html
    Coments:	Links lead to a description, from which there is access to the resource itself. The parent site, Bioinformatics world, has links organized by topics.

  • Life Science Directory

    Name:	Life Science Directory (formerly known as Amos' WWW links page)
    Description:	Portal to databases, organized by topics.
    Source:	http://www.expasy.org/links.html
    Coments:	Includes links to protocols, databases, dictionaries, publishers.

• Graphing and Statistics
  • VENNY

    Name:	VENNY
    Description:	Produces Venn diagrams for up to 4 lists or categories.
    Source:	http://bioinfogp.cnb.csic.es/tools/venny/index.html
    Coments:	So easy, so useful. Graphic is easily downloaded.

  • JMP

    Name:	JMP
    Description:	Complete statistics and graphing software.
    Source:	NEI license: http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Comment:	Powerful mathematical software made accessible to the beginner via extensive and well-done help screens and tutorials.

  • Tableau

    Name:	Tableau
    Description:	Program for information display and high volume data exploration.
    Source:	NEI license: http://neiwapps.nei.nih.gov:6080/compserv/SoftwareRequest.jsp
    Coments:	Tableau does amazing things with spreadsheet data.

• Draw Chemical Structures
  • Advanced Chemistry Development

    Name:	Advanced Chemistry Development
    Description:	Make do novo drawings of organic molecules, including DNA.
    Source:	http://www.acdlabs.com/download/chemsk.html
    Coments:	Extensive set of excellent tutorials. Program must be downloaded.

• Recommendations for Single Purchase software
  • Statistics and drawing

    Name:	Stat-Ease
    Description:	Software for optimizing processes and experimental design.
    Source:	http://www.statease.com
    Coments:	Excellent software, very easy to use. A basic understanding of DOE (Design of Experiment) is needed, but DOE will save tons of time and improve outcomes for almost any process.

    Name:	Inspiration
    Description:	Develop ideas and organize thinking using flow charts, mind maps, and outlines.
    Source:	Single license purchase, $75/each, from http://www.inspiration.com/
    Coments:	The most wonderful program for diagramming and organizing projects. Highly recommended.

    Name:	Partek
    Description:	Software for analyzing microarray data and other large data sets using statistical methods, including T-tests and ANOVA.
    Source:	http://www.partek.com/
    Coments:	Fast, easy-to-use, full-function statistics package. Great software for constructing large tables. Excellent at merging and manipulating tables. Includes highly sophisticated tools for graphical display.