Competency information
Details
Take a DNA sequence and use standard bioinformatic tools to locate within a genome, annotate and infer function, including gene prediction, transcription factor (TF) analysis, splice-site boundaries potential for copy number variants (CNVs).
Considerations
- The genome sequence resources available.
- The annotations provided by genome resources.
- The different types of DNA sequence in databases – complete genome, cDNA, expressed sequenced tags (ESTs), function non- coding sequences.
- Tools for DNA sequence alignment, including those for matching large genomic sequences.
- Resources for non-coding functional genomic regions (databases of transcription factor binding sites, CNVs etc.)
- Resources for alternatively spliced genes.
- Tools for exon prediction – sequence based.
- Tools for exon prediction – signal based.
- Tools for transcription factor (TF) prediction.
- The use of literature resources to support function prediction.
- The processes of combining predictive tools to provide evidenced protein function.
- Best practice guidelines and QA (both internal and external).
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 1 | Outcome Perform analysis on DNA data and protein sequence data to infer function. |
| # 2 | Outcome Perform sequence alignment tasks followed by clustering and phylogeny. |