Csc334 DT Notes

Notes taken by DT, Summer of 08

Source Bioinformatics for Dummies

Background

• Bioinformatic tools (p. 27) mainly fit in 3 categories
  • Sequence alignment
  • Phylogenetic and classification methods
  • Display tools

• Some bioinformatic tasks (could be labs)
  • finding which genomes are available
  • analyzing sequences in relation to specific genomes
  • displaying genomes
  • ORFing: parsing a microbial genome sequence
  • GenScan: parsing a eukaryotic genome sequence
  • finding orthologous and paralogous genes
  • finding repeats

• where to find protein sequences?
  • PubMed, but can be confusing
  • ExPASy (created by Aimos Baroch)

• The FASTA Format:

>  description line
ACGTTTAGGGCTTTAAAA
AAAGGGTCGATTATTTTA

Aligning Sequences

• Use BLAST.
• Find paper explaining why aligning sequences can be useful.
• From Wikipedia entry on BLAST

Examples of other questions that researchers use BLAST to answer are:

Which bacterial species have a protein that is related in lineage to a certain protein with known amino-acid sequence?

Where does a certain sequence of DNA originate?

What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined?

References/Papers

• [1] BLAST Sequences Aid in Genomics and Proteomics, by Dr. Richard M. Casey Published: October 11, 2005