Difference between revisions of "Csc334 DT Notes"
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Source ''Bioinformatics for Dummies'' | Source ''Bioinformatics for Dummies'' | ||
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* Bioinformatic tools (p. 27) mainly fit in 3 categories | * Bioinformatic tools (p. 27) mainly fit in 3 categories | ||
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::: Where does a certain sequence of DNA originate? | ::: 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? | ::: What other genes encode proteins that exhibit structures or motifs such as ones that have just been determined? | ||
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| + | ==References/Papers== | ||
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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 | ||
Revision as of 19:32, 7 July 2008
Contents
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?
- Examples of other questions that researchers use BLAST to answer are:
References/Papers
- [1] BLAST Sequences Aid in Genomics and Proteomics, by Dr. Richard M. Casey Published: October 11, 2005
