Learning objectives:

1. Literature retrieval using PubMed at ncbi.nlm.nih.gov
2. DNA sequence retrieval using Entrez .
3. Using EditSeq (DNAStar) for DNA sequence analysis.
4. Multple sequence alignment.
5. PCR primer design.

1. Introduction
1. Chlamydia spp. and their biological significance.
2. Major outer membrane proteins (MOMP) of Chlamydia spp.
3. Molecular typing using restriction fragment length polymorphism (RFLP).
2. Retrieval of literature
1. Use MEDLINE in PubMed at ncbi.nlm.nih.gov
2. Search for information on the above.
3. Write a short essay
3. Retrieval of DNA sequences.
1. Use Nucleotide databases in ENTREZ.
2. Search for "Major outer membrane proteins and Chlamydia".
4. Install DNASTAR.
5. Open EDITSEQ in DNASTAR.
1. Open "New DNA sequence".
2. Copy and past DNA sequence from ENTREZ search to EDITSEQ.
3. Save each sequence as a separate file in EDITSEQ.
6. Open MEGALIGN in DNASTAR.
1. Enter sequences from (5).
2. Align by Clustal.
3. Edit alignment, if necessary.
4. View phylogenetic tree.
5. View Sequence Distances.
6. View alignment report and display the conserved regions in the aligned sequences.
7. Open PRIMERSELECT in DNASTAR.
1. Enter sequence of template.
2. Enter primer sequences (identified from conserved regions of the multiple sequence alignment).
3. View amplification summary.
4. Describe the best primer pair and the conditions for PCR.