Useful Links

• Finding a Masters or a Ph.D program abroad

• Finding a job abroad

• Bioinformatics Jobs

• Nature jobs search Engine

• Finding Masters/PhD/Job in UK

Online Journals

List of Bioinforrmatics, Functional Genomics, and Related Journals

• Artificial Intelligence

• Artificial Intelligence in Medicine

• Bioinformatics

• Bioinform Newsletter

• BMC Bioinformatics

• BMC Genomics

• BMC Medical Genomics

• BMC Systems Biology

• Briefings in Bioinformatics

• ChemBioChem

• Current Biology

• Current Opinion in Genetics & Development

• Current Opinions in Structural Biology

• Data Mining and Knowledge Discovery

• Drug Discovery Today

• EMBO Journal

• Genome Biology

• Genome Research

• Human Genome News

• In Silico Biology

• Journal of Biomedical Informatics

• Journal of Biomedical Science

• Journal of Computational Biology

• Journal of Machine Learning Research

• Journal of Molecular Biology

• Journal of Molecular Graphics and Modelling

• Journal of Molecular Microbiology and Biotechnology

• Journal of Molecular Modelling

• Journal of Structural and Functional Genomics

• Machine Learning

• Metabolic Engineering

• Nature

• Nature Biotechnology

• Nature Cell Biology

• Nature Genetics

• Nature Molecular Cell Biology

• Nature Molecular Systems Biology

• Nucleic Acids Research

• OMICS: A Journal of Integrative Biology

• Online Journal of Bioinformatics (OJB)

• Physiological Genomics

• PLoS Biology

• PLoS Computational Biology

• PLoS Genetics

• PLoS One

• Proceedings of the National Academy of Sciences

• Proteomics

• Protein Engineering

• Protein Science

• Proteins: Structure, Function, and Genetics

• PSB On-Line Proceedings

• Science

• The Scientist

• Structure

• Trends in Biochemical Sciences

• Trends in Biotechnology

• Trends in Genetics

• Trends in Molecular Medicine

• Trends in Pharmacological Sciences

Bioinformatics Tools and Resources

Bioinformatics Centers

EBI - European Bioinformatics Institute

EMBL - European Molecular Biology Laboratory

ExPASy - Molecular Biology server

NCBI - National Center for Biotechnology Information

Entrez - Browse a subset of MEDLINE, and the NCBI protein and nucleotide databases

Centre for Integrative Bioinformatics VU, The Netherlands

CBS, Center for Biological Sequence Analysis, Technical University of Denmark

BIBISERV, Bielefeld University Bioinforrmatics Server

BSM, Biomolecular Structure and Modelling at UCL

Human Genome Project Information

Sanger centre, Hinxton, England

UK MRC HGMPRC UK Human Genome Mapping Project Resource Centre

DDBJ DNA data bank, Japan

GDB Genome Data Base

HUM-MOLGEN Human Molecular Genetics

Centre of Bioinformatics, Peking

Microarray Data Analysis

Microarray software Suite TM4 this suite includes the following (free for download) packages:

• 1. MADAM: MicroArray DAta Manager (facilitates the entry of microarray data into a relational database)

  2. Spotfinder (analysis of microarray images)

  3. MIDAS: Microarray Data Analysis System (normalization and filtering of microarray data)

  4. MeV -Multi-Experiment-Viewer (Includes several methods for analysis of microarray data)

Database Searching

BLAST Server Sequence searches at NCBI

Bioccelerator - Sequence searches at EMBL

Database searches at EBI

Database searches at DISC (Japan) - includes Fasta, BLAST, MPsrch and SRS Fasta

Match sequence against PROSITE

Multiple Sequence Alignment

PRALINE multiple sequence alignment

T COFFEE multiple sequence alignment

Clustal W multiple sequence alignment

SAM, Sequence alignment and modeling system (using HMMs)

AMAS Analysis of multiple alignments (Geoff Barton)

HMMER multiple sequence alignment

DIALIGN 2 multiple sequence alignment

Secondary Structure Prediction

PredictProtein - Server to predict protein structure

PSI-Pred - PSI-BLAST-based protein secondary structure prediction

YASPIN - Server to predict protein secondary structure

Modelling and Data analysis

DALI - Comparison of protein structures in 3D

Pratt - pattern discovery online

Expression Profiler - online tool for expression profile clustering and sequence pattern discovery

PSA, Protein Sequence Analysis: fits a structure model to your sequence

Block Maker, at Fred Hutchinson Cancer Research Center

MEME, Multiple EM for Motif Elicitation