logoCIC          

Bioinformatics and Functional Genomics Research Group
Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca (SPAIN)

Dr. Javier DE LAS RIVAS
Sara AIBAR - Celia FONTANILLO - Yerae MARTÍN - Beatriz ROSÓN
Former Members (Carlos PRIETO - Alberto RISUEÑO)

RESEARCH AREAS:  Bioinformatics,  Functional Genomics,  Proteins and Proteomes,  Systems Biology
RESEARCH TOPICS:  Genome-wide analysis of expression profiles
,
Protein interactions and interactomes


Main Bioinformatics Research Centers (USA & EUROPE):
NCBI The National Center for Biotechnology Information at NIH, USA
EBI The European Bioinformatics Institute in Cambridge, UK

Web Links to Bioinformatics and Structural Biology:


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GENOME PROJECTS

Human Genome Project
Joint Genome Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
The Sanger Centre The Sanger Centre, Hinxton, U.K.
BROAD Institute BROAD Institute, MIT and Harvard, Cambridge, MA, USA
Washington Univ. Genome Seq. Center Washington University Genome Sequencing Center, St. Louis, MO, USA

Non-Human Genome Projects
Mouse MGI Mouse Genome Informatics
C. elegans Wormbase
Drosophila  Flybase
Rat Ratmap
Saccharomyces SGD Saccharomyces Genome Database
Human GenomeTop

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PROTEIN ANALYSIS

 Sequence search / alignments

SRS-EBI SRS WWW server at EBI, Hinxton, UK., version 6.0.6
Swiss-Prot Access to SWISS-PROT and TrEMBL (ExPASy, CH)

ORF Finder Open Reading Frame Finder (NCBI)
Blast2_EMBL WU-BLAST2 search at EMBL (blast 2.0 with gaps)
Blast2_EBI WU-BLAST2 search at EBI (blast 2.0 with gaps)
Blast2_NCBI Basic/Advanced BLAST  (blastall)  search at NCBI
FASTA3_EBI FASTA3 at EBI

ClustalW_EBI ClustalW2 Server at EBI

SAM_Home SAM: Sequence Alignment and Modeling System (HMM)
SAM_applications UCSC HMM Applications
ISMB99 tutorial on using HMMs  Making the most of your hidden Markov models
NAIL Network Analysis Interface for Linking HMMER results (EMBL)

AQUA AQUA - Alignment Quality Assessment (EMBL)
Protein analysisTop

Primary structure
 
InterPro Integrated resource of protein domains and functional sites (EBI, UK)
SMART Simple Modular Architecture Research Tool. Domains/motif  detection (EMBL)
SignalP Predicts the presence and location of signal peptide (CBS, DK)

PredictProtein The PredictProtein server  (Columbia, USA)
ExPASy Tools ExPASy Proteomics tools
Protein analysisTop

Secondary structure
 
COILS Prediction of Coiled Coil Regions in Proteins (ISREC, CH)

PredictProtein The PredictProtein server  (Columbia, USA)
ExPASy Tools ExPASy Proteomics tools
Protein analysisTop

Tertiary structure / Threading
 
Swiss-Model SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH)
UCLA-DOE UCLA-DOE Fold-Recognition server (UCLA, USA)

PDB - RCSB Protein Data Bank (RCSB)
PDBsum Summaries and structural analyses of PDB data files (UCL, UK)

SCOP Structural Classification of Proteins (MRC-LMB, UK)
CATH CATH Protein Structure Classification (UCL-BSM, UK)
FSSP Fold classification based on Structure-Structure alignment of Proteins (FSSP) (EBI)
Protein analysisTop

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PATWAYS

KEGG KEGG:Kyoto Encyclopedia of Genes and Genomes (ICR, JP)
REACTOME Reactome is a database of biological pathways
 

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BIBLIOGRAPHY

PubMed PubMed is the National Library of Medicine's search service 
   
Science The EMBO Journal Bioinformatics
Nature Journal of Biological Chemistry Journal of Molecular Biology
Nature Biotecnology Current Opinions Online
Nature Cell Biol. Annual Reviews Protein Science
Nature Genetics Molecular Cell  Protein Engineering
Nature Struct. Biol. Molecular and Cellular Biology  Proteins: Struc. Func. and Bioinformatics
Cell Nucleic Acid Research  
Proc. Natl. Acad. Sci. USA FEBS Letters BBA
   

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Copyright
Javier De Las Rivas
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Last update: August, 2011.