Difference between revisions of "Csc334 DT Notes"
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* [http://www.b-eye-network.com/view/1730] BLAST Sequences Aid in Genomics and Proteomics, by Dr. Richard M. Casey Published: October 11, 2005 | * [http://www.b-eye-network.com/view/1730] BLAST Sequences Aid in Genomics and Proteomics, by Dr. Richard M. Casey Published: October 11, 2005 | ||
| + | * [http://news.bbc.co.uk/1/hi/sci/tech/3161336.stm] Volcanic blast recorded in DNA, Jonathan Amos, BBC News Online science, 3 October, 2003 | ||
Revision as of 19:37, 7 July 2008
Notes taken by DT
--Thiebaut 00:33, 8 July 2008 (UTC)
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?
- Examples of other questions that researchers use BLAST to answer are:
