LSM2104 Practicals Essential Bioinformatics and Biocomputing 2002

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• Part II Lecturer:
  Assoc Professor Tan Tin Wee
  Department of Biochemistry, NUS
  [Namecard | Bio | BIC-HQ | Tel. 9664-0347 | Email: tinwee@bic.nus.edu.sg ]
   
• Teaching Assistants:
  Justin Choo, NUSIBILL 1, Dept of Biochemistry, NUS
  Bhuvana, NUSIBILL 1, Dept of Biochemistry, NUS
  Cao Zhiwei, CZ, NUS
  Chen Xin, CZ, NUS
  Manisha Brahmachary, BIC-LIT, NUS
  Ms Lim Yun Ping, Lab Manager, NUSIBILL 2, Dept of Biol Sci, NUS
  Their email addresses are the same as found in the IVLE LSM2104

1. Project Admin and Research Instructions | HTML | WordDoc | PDF |
2. Practical MiniProject Report template
3. Create Your Personal Directory (do this only once)
4. Upload Site For Students' WebPages
5. Frequently Asked Questions (FAQ)


6. Help in Creating HTML Web pages:
   • Ravi Chandran's HTML course (please self-learn before your practical)
   • Search Google.com with keywords "HTML tips" or "HTML Tutorial" etc.
7. Useful PC software which might be of help to you.
   They are all intuitive and have comprehensive help documentation that will guide you through its usage. Just keep an open mind, trial and error, test and use, and you should be able to pick up the usage of the software.
   • DNAStar - may still be available under NUSNet Windows Shopping
   • Vector NTI - accessible via NUSNet Windows Shopping (Expert: yunping@bic.nus.edu.sg) from Informax Inc.
   • BioEdit - version 5.0.9 (free software for Win95/98/NT/2000) by Tom Hall
     Read the review
8. Where to do your BLAST Searches (Pls use local site first)
   • Local BLAST SITE for B.pseudomallei (search for chromosome 1 and 2 separately : bug temporarily fixed)
     Please use the local site first
   • Sanger Centre BLAST site for B.pseudomallei (use this for combined Chrom 1 AND 2 searches)
9. Where to do other data manipulation and other types of bioinformatics applications?
   • Local site for Extraction of subsequences from Chromosome 1 or Chromosome 2 of the genome based on the start and end residue number.
   • Local site for Reverse Complement of sequences from Extracted sequences in the previous step.
   • Local site for Translation of sequences from Extracted sequences in the previous step.
   • Local site for translation and finding Open Reading Frames (ORF) of nucleotide sequences from Extracted sequences in the earlier step (alternative to the "Translate" program.
   • Local site for CLUSTALW Simple multiple sequence alignment.
10. Where to get other useful info?
    • Examples of genes found in Chromosome 1 and 2 of B.pseudomallei: master list
    • Taxonomy of Burkholderia genus from NCBI (useful for Step 2 in finding other species related to B.pseudomallei within the genus.

Lectures will be held on Mondays from 2-4pm at LT32, National University of Singapore

1. TTW Lecture 1 2 Sep 2002
2. TTW Lecture 2 16 Sep 2002
3. Blast at NCBI Adapted from Peter Cooper, NCBI
4. TTW Lecture 3/4 24 Sep 2002

Practicals will be held on Tuesdays at three locations

Continual Assessment is in the form of a Practical Web Report

Unsolicited Student Feedback New! Thanks for your kind comments! ttw

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Last Updated : 21 Sep; 16 Sep; 30 Aug 2002 TTW
First Created 30 Aug 2002 - Dr Tan Tin Wee