Biochemistry 201

Advanced Molecular Biology

Bioinformatics:

Determining Function from Sequence

Doug Brutlag

Homework Assignment

Literature References

• General Books
• General Reviews
• Molecular Databases on the Internet
• Consensus Pattern Matching
• Quantitative and Probabilistic Pattern Matching
• Alignment of Biological Sequences
• Similarity Scoring Systems
• Rapid Sequence Similarity Search

Bioinformatics Courses

• Algorithms and Representations in Computational Molecular Biology (Computer Science 274/Medical Information Science 214)
• Computational Molecular Biology (Biochemistry 218/Medical Information Sciences 231)
  • Microsoft Media Player
  • Computational Molecular Biology Online
• Protein Architecture, Dynamics and Structure Prediction (Structural Biology 228)

Molecular Biology Resources

• Bioinformatics Resource
• Brutlag Group's Home Page
• Brutlag Group's Bookmarks

Molecular Biology Databases

• European Bioinformatics Institute
• ExPASy Molecular Biology
  • Swiss-Prot
  • Prosite
  • Sequence Analysis Tools
• Molecules R Us
• National Center for Biotechnology Information (NCBI)
  • Entrez
  • PubMed
  • OMIM
• National Human Genome Research Institute
• Protein Data Bank (PDB)
• Protein Identification Resource (PIR)
• TIGR Genome Databases

Consensus Pattern Matching Sites

• Prosite Home Page
• Prosite Scan (Expasy)
• EMOTIF-Maker
• EMOTIF-Search
• EMOTIF-Scan

Blocks Database and Searching

• Blocks Server
• Block Maker
• Block Searcher
• EMATRIX-Maker
• EMATRIX-Search
• EMATRIX-Scan

Alignment and Similarity Search

• BLAST at NCBI
• BLAST, Smith Waterman, HMM on Decypher Hardware
• Multiple Sequence Alignment Methods
• Multiple Sequence Alignment Tutorial
• Multiple sequence alignment (Clustal) on Decypher

Hidden Markov Model Database and Search

• HMM Pfam homepage
• HMMer (Eddy)
• pFAM and HMM searches on Decypher

Protein Fold and Domain Databases

• CATH Classification of Proteins, UCL BSM
• Dali Server (EMBL)
• PROF Form
• DSSP Program and Database
• HSSP Database
• Structural Classification of Proteins (SCoP)

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