Difference between revisions of "Csc334 DT Notes"
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* From Wikipedia entry on BLAST | * From Wikipedia entry on BLAST | ||
::Examples of other questions that researchers use BLAST to answer are: | ::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? | + | :::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? | + | ::: 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? |
Revision as of 19:23, 7 July 2008
Notes taken by DT, Summer of 08
Source Bioinformatics for Dummies
- 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:
