Difference between revisions of "Csc334 DT Notes"
| Line 17: | Line 17: | ||
** finding orthologous and paralogous genes | ** finding orthologous and paralogous genes | ||
** finding repeats | ** finding repeats | ||
| + | |||
* where to find protein sequences? | * where to find protein sequences? | ||
** PubMed, but can be confusing | ** PubMed, but can be confusing | ||
** ExPASy (created by Aimos Baroch) | ** ExPASy (created by Aimos Baroch) | ||
| + | |||
* The FASTA Format: | * The FASTA Format: | ||
| Line 28: | Line 30: | ||
| − | * ? | + | ==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? | ||
Revision as of 19:22, 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?
