Computational Biology Home

REVIEW:  Basic Chemistry

REVIEW:  Bioorganic Chemistry

PRIMER:  Molecular Biology
 
 

Introduction to Genomics Features of genomes coding DNA non-coding DNA Teleological Implications Definitions of the Gene Genomics comparative functional Genome sequencing projects Bioinformatics (data bases and annotation) Proteomics Structural Biology Phylogenetic Analysis and Evolution Some Basic Tools for Computational Biology Search Techniques for the WWW Bare bones of computer searches Search Engines for the Web   Excel Tutorial Introduction to Data Mining Introduction to the NCBI  Data Bases and ENTREZ The Bookshelf OMIM Introduction to PubMed Sequence Data Bases and Formats The Gene Data Base NCBI Nucleotides Data Base GenBank Flat files and formats Dissection auxin gene The RefSeq Data Base Other Data Bases The NCBI Protein Data Base Cancer Chromosomes OMIA SNP Introduction to Sequence Similarity Searches and BLAST. Obtaining a FASTA sequence BLAST Queries Understanding Conserved Domains Understanding the BLAST hit list. Introduction to Multiple Alignment and Phylogenetic Analysis. The Biology Workbench at San Diego Supercomputer Center BLASTP CLUSTALW BOXSHADE Phylogenetic Trees (DRAWTREE and DRAWGRAM) Protein Structure Data Bases and 3D Viewers. REVIEW:  Protein Structure and Function. 3D Visualization of DNA structure. 3D Structure and Function of Hemoglobin Protein Structure Databases.   NCBI Genome Database and Genome Maps Sequencing and Mapping Gene nomenclature Low resolution mapping recombination mapping break point mapping radiation hybrid mapping High Resolution mapping STSs and ETSs BACs and YACs Sequencing and Contig Assembly Annotation ENTREZ:  Genomic Biology and Map Viewer Organism Resources Map Viewer Genome-wide searches Chromosome-specific searches Maps available Map queries Chromosome Launchpad

Comparative Genomics, Sequence Alignments and Phylogenetic Analysis. PRIMER:  Evolutionary Biology Theory of optimal alignments Application of Dynamic Programming DOTTER Matrices of log-odds scores (substitution matrices) Statistics and Significance of the Alignment Computer applications of Smith-Waterson Algorithm LALIGN FASTA PRSS PHYLIP         Biology Workbench Nucleotide Tools Ndjinn ORF Finder Translator Restriction Sites PCR primers  (Primer 3) Protein Structure databases and Molecular Modeling PRIMER: Physical Chemistry of Proteins X-Ray Crystallography Principles Rosalind Franklin and DNA Max Perutz and Hemoglobin PDB and MMDB files Structure Viewers DeepView Cnd3 VAST Protein Explorer Motifs, Fingerprints and Families of Proteins PROSITE PFAM FINGERPRINTSCAN SAPS PATTERNMATCH