The final section
By now you have:
- Completed a series of BLAST
searches. - Completed a search of Prosite (ppsearch), Interpro, Pfam, and SMART sites.
- Found an entry for a protein in the OMIM database.
- Found the DOI for a paper.
- Found a paper for a given DOI.
- Revisited the wiki.
- Taken a short tutorial on plagiarism.
In this section of the practical we are going to:
- Revisit the PubMed system
- Expand upon your previous experience of SMART and Prosite searches.
- Identify a protein, retrieve information on the protein structure, secondary modifications, and function, using a peptide sequence.
In
PubMed we will:
- Start with a key term (or terms) to find book articles/papers/protein/ DNA sequences associated with the terms using Entrez
- Take a short, incomplete reference (the sort of reference flashed up on a screen in a lecture) find the paper/protein/DNA sequences associated with the paper using PubMed
Starting with a protein sequence, we will:
- Use BLAST searches to identify the protein
- Identify functional sites in the protein using SMART
- Identify functional domains in the protein with Prosite
- Identify functional sites in the protein using Interpro
- Identify functional sites in the protein using Pfam
You should then be ready to tackle the assessment.