Comprehensive Guide to Bioinformatics Resources for Biochemistry Research

1. Bioinformatics I Stephen Tsui Biochemistry

2. Information Acquisition

3. Sources of Literature • Books in NCBI Currently 61 books on the shelf http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books&itool=toolbar • Selected Biochemistry-related books Molecular Cell BiologyGenomes Molecular Biology of the Cell Biochemistry Modern Genetic Analysis Retroviruses Introduction to Genetic Analysis Immunobiology Genes and Diseases Neurosciences Human Molecular Genetics 2 Developmental Biology Sequence-Evolution-Function Basic Neurochemistry The Cell – A Molecular Approach Endocrinology

4. Where can I get an article? • PubMed in NCBI More than 16 million citations from MEDLINE. For PubMed Central articles or journal articles that have been subscribed by our University, the full-text PDF files could be downloaded from the Web. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed • Electronic journals http://www.lib.cuhk.edu.hk/electronic/jol.htm • The corresponding author of the article • Friends in other institutions

5. Important Notes for Downloading Articles from the Web • Don’t post the PDF files on Web • Be careful when you distribute a downloaded article • Prevent systematic download of a whole issue or all issues of a journal • Print out articles only if you plan to read them • Sort your articles into different folders in your computer • Name your articles by their titles

6. How to Conduct a Comprehensive Literature Search? • Be familiarized with the PubMed by browsing the PubMed tutorial http://www.nlm.nih.gov/bsd/disted/pubmed.html • Type the keywords in the PubMed page http://www.ncbi.nlm.nih.gov/entrez/query.fcgi e.g. SARS AND spike AND receptor • Save the abstracts in a text format • Read the abstracts and remove unrelated records • Download the essential PDF files and read the most recent review to have an overview of the issue.

7. ENTREZ • Entrez integrates the scientific literature, DNA and protein sequence databases. http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi • Properly use “AND”, “OR”, “NOT” and “[ti]” strings

8. Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders. The team has done an excellent job in summarizing and updating information about genes and diseases. Example: Genetic disorders: Lung cancer, AIDS Genes: p53, FHL2

9. Taxonomy Browser http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=TAXONOMY The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. Examples: Mus musculus, Bos taurus, Mycoplasma genitalium

10. Protein-Protein Interaction Databases • Protein-protein interactions could be experimentally revealed or computer predicted. Both of them have important implications on the protein functions. For example: MIPS Protein-Protein Interaction Database http://mips.gsf.de/proj/ppi/

11. Genome Biology • Selection of organism specific genomic databases: Human -http://www.ncbi.nlm.nih.gov/genome/guide/human/ Mouse -http://www.informatics.jax.org/ Drosophila malanogaster -http://flybase.bio.indiana.edu/ Caenorhabditis elegans -http://www.wormbase.org/ Escherichia coli -http://www.ecocyc.org/ Saccharomyces cerevisiae -http://www.yeastgenome.org/

12. Bioinformatics

13. Four Golden Rules for Bioinformatics Analysis • Use published tools, which are more reliable. • Read the user manual to learn the proper use and limitations of the tools. • Look for the information that is helpful for the interpretation the results. • Use more than one tools with the same function to cross validate the results.

14. Four Major Sites as Good Starting Points • National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/ • European Bioinformatics Institute (EBI) http://www.ebi.ac.uk/Information/ • Biological Information Resource (BIR) http://courses.washington.edu/bioinfo/BIR/ • ExPASy Proteomics Server http://ca.expasy.org/

15. Biological Information Resources http://courses.washington.edu/bioinfo/BIR/ • Biological Information Resources (BIR) is an excellent portal for the access of commonly used bioinformatics tools.

16. DNA Analysis Tools • Codon usage http://bioinformatics.org/sms2/codon_usage.html Example: p53 mRNA

17. DNA Analysis Tools • Restriction site analysis For example: WebCutter http://www.firstmarket.com/cutter/cut2.html Example: p53 mRNA

18. DNA Analysis Tools • Primer analysis For example: Primer 3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Example: p53 mRNA

19. Protein Analysis Tools • Statistical Analysis of Protein Sequences http://www.isrec.isb-sib.ch/software/SAPS_form.html Example: p53 protein, insulin receptor

20. Protein Analysis Tools • Hydrophobicity plot http://expasy.ch/cgi-bin/protscale.pl Example: p53 protein, insulin receptor

21. Protein Analysis Tools • Isoelectric point and molecular weight Example: p53 protein, insulin receptor

22. Protein Analysis Tools • Protein Subcellular Localization Prediction http://wolfpsort.seq.cbrc.jp/ Example: p53 protein, insulin receptor

23. Protein Analysis Tools • Transmembrane region and orientation DAS - http://www.sbc.su.se/~miklos/DAS/ Sosui - http://bp.nuap.nagoya-u.ac.jp/sosui/ Example: p53 protein, insulin receptor