Use the UCSC genome browser to get the gene symbol and the protein sequence for the gene assigned to you: Bioinformatics in Genetic and Protein Analysis Course Work, UCC, Ireland
| University | University College Cork (UCC) |
| Subject | Bioinformatics in Genetic and Protein Analysis |
Tasks
- Use the UCSC genome browser to get the gene symbol and the protein sequence for the gene assigned to you. It is also important to start with the canonical/most evolutionary conserved isoform of the gene.
- Building a multiple sequence alignment – carefully select orthologous sequences. This is a bit of hit and tries approach. Initially, there is a pool of several sequences in the alignment, but you have to progressively
filter down and get rid of sequences that have a very long N-terminus or C-terminus. Eventually, you will generate a multiple sequence alignment that has to copy into the text file and then submit this text file together with your
assignment. - Find the domains in your sequence using Interpro. Feel free to use other domain detection/prediction tools as well. You can supplement your report with predictions from additional tools
- Use at least 2 different secondary structure prediction tools and discuss if the predicted secondary structures are in agreement with each other or not.
- This is done using the Swiss Model. Discuss some of the details of the tertiary structure that the Swiss Model predicts. If this is a good structure (based on some of the metrics that we have covered such as the Ramachandran Plot). It could also be that someone already determined the 3D structure of your protein. Report this information accordingly.
- Write a one/two page summary about the gene assigned to you. gene cards are a good starting point. Do not copy the text from gene cards. The purpose of this task is that you learn about one human gene – what it does in terms of its molecular function, and whether it is implicated in disease. Furthermore, you could look for information related to your gene on OMIM. But these are just guidelines, feel free to add more information about your gene from some other database or from published literature.
- You could use both – the UCSC genome browser and Ensembl to assess whether the gene is conserved or not. However, additional information such as screenshots from either of the two resources to support your answer.
