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Project 1
Biology 398INA: Topics in Bioinformatics
Project # 1: Characterizing a gene family by means of bioinformatics
Due March 14, 2003
"project1.doc"
Pick a gene by name, and run it through the entire suite of procedures.
Either find the orthologues from at least 10 different species, or find at
least 10 different paralogues from the same species (note, mutations consisting
of just a few bases don't count as paralogues for this assignment)!
Entrez to find one
- BLAST/FASTA to find homologues
- BLOCKMAKER, PFSCAN or other programs to find conserved regions
- PSI-BLAST, COBBLER, LAMA to find more distant homologues
- VAST & combinatorial extension to find related genes by structure
- ClustalW and other multiple sequence alignments to find and highlight conserved
regions
- PHYLIP to construct phylogenies using these multiple alignments:
- One based on distance matrix methods
- One based on maximum parsimony
- One based on maximum likelihood (you may need to use DNA sequences
for this)
- Evaluate your trees
- bootstrap analysis
- shuffling order or other online resources
- Use MacVector or Primer3, etc to design primers to study gene in populations
- Pick an organism that has genomic sequence including your gene, then use
Genefinder, etc to find nearby genes in genomic DNA
- CODEHOP to design primers to fish out related genes from cDNA of a new
organism
- Design a protocol for cloning the coding sequence of one of these genes
into Bluescript
- Identify ORF
- Design primers to cut as close to start & stop as possible, evaluate
them using MacVector or primer finder
- Describe procedure for performing the cloning, including restriction
enzymes used, how you will prepare DNA, and print map of recombinant plasmid
- print 50 bp of sequence at the junctions between the plasmid and cloned
DNA
Report: email me the results for each of these tests
Suggested Paralogues (i.e multi-gene families within an organism)
- Globins
- Steroid receptors
- keratin
- Cytochrome P-450
- DEAD box
- Sodium channel
- Leucine Zipper proteins
- Myosin
- Actin
- Multi-drug resistance
- Porins
- Integrins
- Tyrosine kinase receptors
- G-protein-linked receptors
- G-proteins
- tripartite motif protein
- Major Histocompatibility Complex proteins
- Homeodomain proteins
Suggested Orthologues (these are trickier, because you can’t be certain
whether you are looking at the correct counterpart unless there is only one
copy of the gene)
- Malonyl-CoA transacylase
- Catalase
- Myoglobin
- Cytoplasmic malate dehydrogenase
- beta-hydroxyacyl-ACP dehydratase
- lauroyl acyltransferase
- HMG-CoA synthase
- HMG-CoA reductase
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