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INBRE Menu
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RI-INBRE > Links >
Bioinformatics Resources
Bioinformatics Resources
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Databases - Genomic
Human Genome Database
International
Nucleotide Sequence Databases
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DDBJ - DNA Data Bank of Japan
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EBI - European Bioinformatics
Institute
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NCBI - National Center for
Biotechnology Information
Other Organism
Databases -
Proteomics
Molecular Modeling
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CATH - protein structure
classification
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DALI - networking services for
comparing protein structures in 3D
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DSSP - definition of secondary
structure of proteins given a set of 3D coordinates
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FSSP - food classification based
on structure-structure alignment of proteins
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HSSP Database -
Homology-derived Secondary Structure of Proteins
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Jpred2 - method for protein
secondary structure prediction
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K2 - protein structure
alignment - various food recognition and local structure
prediction methods
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PDB - processing and distrubutio
of 3D biological macromolecular structure data
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PredictProtein & PHD - service
for sequence analysis, and structure prediction
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PSIpred (& MEMSAT & GenTHREADER) -
protein structure prediction server
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RasMol / Protein Explorer -
software for viewing macromolecular structure
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SCOP - Structural Classification
Of Proteins
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Structure Prediction Meta-server
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SWISS-MODEL - protein modeling
server
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The DALI Domain Database -
structure classification of protein domains
Protein Sequence
Databases
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MIPS - Munich Information
centre for Protein Sequences
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PIR - Protein Information Resource
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SWISS-PROT & TrEMBL - protein
sequence knowledge database and computer annotated supplement
Databases of Gene
Regulation and Cell Signaling
Gene Expression dasfd
Gene Regulation
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Cister - cis-element cluster
finder
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DBTSS - database of
transcriptional start sites
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DCPD - Drosophila Core
Promoter Database
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DPInteract - DNA protein
binding sites within E. coli DNA
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EPD - eukaryotic promoter
database
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Kimono - find regulatory
elements in promoter sequences
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MatInspector - locate
transcription factor binding sites
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PromoterInspector - prediction
of promoter regions in mammalian genomic sequences
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SCPD - promoter database for
Saccharomyces cerevisiae
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TRANSFAC - the transcription
factor database
Signal Transduction
and Cell Signalling
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Alliance for Cellular Signalling
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BIND - Biomolecular
Interaction Network Database
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CSNDB - Cell Signalling
Networks Database
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DIP - Database of Interacting
Proteins
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KEGG - Kyoto Encyclopedia of
Genes and Genomes
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PathDB - research tool for
biochemistry & functional genomics
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PFBP - Protein Function and
Biochemical Pathways Project
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SPAD - Signaling Pathway
Database
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stke - Signal Transduction
Knowledge Environment
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Transpath - information system
on gene regulatory pathways
Other Resources
Searching and
Tools - Genomics
Sequence Alignment
Sequence Similarity
Tools - Proteomics
Protein Domain
Families
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Blocks - a service for
biological sequence analysis
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InterPro - resoure for protein
families, domains, and functional sites
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Pfam - multiple sequence
alignments and hidden Markov models
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PRINTS Database - protein finger
prints database
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ProDom - protein domain database
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PROSITE - database of protein
families and domains
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Protein Domain Profile Analysis @ BMERC -
search a library of functional
diagnostics profiles with a protein sequence
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SMART - simple modular
architecture research tool
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TIGRFAMs - protein families based
on Hidden Markov Models
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News & Events
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Newsletter |
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RI-INBRE Newsletter Winter 2013
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Grant Workshop PowerPoint Presentations &
Handouts |
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Balancing Teaching and Research at PUIs
Components of a Successful AREA (R15) Grant
NSF-RUI Program:
Strategies and Tips for Success
Handouts
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Important Dates & Announcements |
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RI-INBRE Calendar
RI-INBRE News
NIH Public Access Policy
NIH R15 Submission Deadlines - June 25, October 25, & February 25
3/22/2013 - "Revealing
Nonobvious Features in Noncoding Human DNA - Insights for Evolution, Gene
Expression and Disease" by Laura Elnitski, Ph.D., National Human Genome
Institute, National Institutes of Health
8/14/2013-8/16/2013 -
5th Northeast
Regional IDeA Meeting, University of Delaware, Newark, DE
4th Northeast Regional IDeA
Meeting, Salve Regina University, Newport, RI
RI Inbre Research Fellows
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