Links to Important Bioinformatics Web Sites For Class Use

    An Introduction to Bioinformatics On-line

    Bioinformatics is a relatively new branch of cell and molecular biology which involves the use of computers and the internet to bank, search and analyse nucleic acid and protein sequences. There are several basic areas within this field: (see below) Click for more information

• Sequence Databases (Genbank, EMBL)
  >Banking and Searching Sequences
  >Linking  sequence information to literature references and other related sequences
  >Linking sequence information to X-Ray chrystalographic structures

• Sequence Analysis (On-line analysis Programs)
  >Alignment of sequences for discovering structural and evolutionary relationships
  >Prediction of secondary and tertiary structure (proteins) based on primary sequence
  >Prediction of protein physical properties (pI, titration curve, molecular mass)
  >Identification of specific features (motifs) for glycosylation, phosporylation, protein-protein interaction
  >Translation of nucleic acid sequences into amino acid sequences
  >Identification of nucleic acid motifs; promoter elements, start codons, termination codons, introns etc.
  >Design of PCR primers
  >Assembly of  "contigs" into contiuous sequences for determining genome structure

• Higher order modeling of protein structure (Computational Bioinformatics)
  >Analysis of  free energy content for projected protein folds etc.
  >Homology Modeling: "threading (superimposing) one sequence over a related sequence

   Sequence Databases:

     National Center For Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/

• ENTREZ - Searches of Nucleic acid or Protein Sequence Databases by key words

• PUBMED- Searches of Medline Database for Literature References by key words

• BLAST- Searches of Nucleic Acid or Protein Databases by finding "matching" sequences

• STRUCTURE- Search the   "Protein Database Brookhaven" (PDB) for Crystal Structures

• TUTORIAL on NCBI BLAST Searching http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/blast.shtml

  Swiss+Prot-EMBL http://www.ebi.ac.uk/swissprot/

• Simple Searches by protein name

• SRS Searches advanced querrys Click here

• Protein Sequence Alignment (tutorial)
  
  Sequence Analysis Programs On-line:

• Biology Workbench (U.C. San Diego Supercomputer)
       You need to create an account of your own then you can save your work

     Standard Log On: Click Here      Student Interface Log On: Click Here

      On-line Worm Links:

• Wormbase click here

• C. elegans WWW server

• Caneorhabdidis II ( Online  C. elegans Reference TOC)

• NCBI/NIH Model Organisms Guide

• Worm Anatomy (Atlas)

• Basic C. elegsans lore

• Worm Literature Index

• Worm Atlas