Difference between revisions of "BIN-EBI"
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | ||
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
| − | *[[BIN-Databases]] | + | *[[BIN-Databases|BIN-Databases (Bioinformatics Databases)]] |
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*Read the introductory notes on {{ABC-PDF|BIN-EBI|the EBI and UniProt}}. | *Read the introductory notes on {{ABC-PDF|BIN-EBI|the EBI and UniProt}}. | ||
}} | }} | ||
| + | |||
| + | {{task|1= | ||
| + | |||
| + | # In the [[BIN-Storing_data]] unit you have found the protein of YFO that is most similar to yeast Mbp1, in YFO. | ||
| + | # Finally access the [http://www.uniprot.org/uploadlists/ UniProt ID mapping service] to retrieve the UniProt ID for the protein. Paste the RefSeq ID and choose '''RefSeq Protein''' as the '''From:''' option and '''UniProtKB''' as the '''To:''' option. | ||
| + | |||
| + | :<small>If the mapping works, the UniProt ID will be in the '''Entry:''' column of the table that is being returned. Click the link and have a look at the UniProt entry page while you're there.</small> | ||
| + | |||
| + | <!-- What could go wrong? Sometimes the mapping does not work: | ||
| + | I don't know why the mapping for some sequences is not available. | ||
| + | If this happens, you can work around the problem as follows. | ||
| + | |||
| + | 1. Load the RefSeq protein page | ||
| + | 2. View the protein as FASTA and copy the sequence. | ||
| + | 3. Open the UniProt BLAST page http://www.uniprot.org/blast/ | ||
| + | (Yes, UniProt runs its own BLAST version, and that searches UniProt databases, not Genbank) | ||
| + | 4. Paste the sequence into the search form and run BLAST. | ||
| + | |||
| + | ... if the sequence is in UniProt, you will get the top hit with 100% sequence identity. In your case it is: | ||
| + | H1VQK3 ( http://www.uniprot.org/uniprot/H1VQK3 ) | ||
| + | |||
| + | I.e. UniProt contains the sequence, but the mapping service does not know. | ||
| + | --> | ||
| + | |||
| + | |||
| + | |||
| + | }} | ||
| + | |||
| + | |||
| + | |||
Revision as of 13:23, 30 September 2017
Databases and services at the EBI
Keywords: The EBI databases and services, Uniprot
Contents
This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.
Abstract
...
This unit ...
Prerequisites
You need to complete the following units before beginning this one:
Objectives
...
Outcomes
...
Deliverables
- Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
- Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
- Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
Evaluation
Evaluation: Integrated Unit
- This unit should be submitted for evaluation for a maximum of 10 marks. Details TBD.
Contents
Task:
- Read the introductory notes on the EBI and UniProt.
Task:
- In the BIN-Storing_data unit you have found the protein of YFO that is most similar to yeast Mbp1, in YFO.
- Finally access the UniProt ID mapping service to retrieve the UniProt ID for the protein. Paste the RefSeq ID and choose RefSeq Protein as the From: option and UniProtKB as the To: option.
- If the mapping works, the UniProt ID will be in the Entry: column of the table that is being returned. Click the link and have a look at the UniProt entry page while you're there.
Further reading, links and resources
Notes
Self-evaluation
If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2017-08-07
Version:
- 0.1
Version history:
- 0.1 First stub
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