biology

PSORTdb

PSORTdb is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand PSORTdb rather than just read about it. In short: PSORTdb is a database of protein subcellular localization (SCL) for bacteria and archaea. It is a member of the PSORT family of bioinformatics tools.

Key takeaways

PSORTdb belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect PSORTdb to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of PSORTdb from memory before moving on to harder problems.

Reference excerpt

PSORTdb is a database of protein subcellular localization (SCL) for bacteria and archaea. It is a member of the PSORT family of bioinformatics tools. The database consists of two datasets, ePSORTdb and cPSORTdb, which contain information determined through experimental validation and computational prediction, respectively. The ePSORTdb dataset is the largest curated collection of experimentally verified SCL data. PSORTdb was initially developed in 2005 in order to contain protein subcellular localization predictions for bacteria. The computational predictions in the cPSORTdb dataset were generated by the PSORT tool PSORTb 2.0, the most accurate SCL predictor of the time. The second and current version of PSORTdb was released in 2010. Entries in the database are automatically generated as newly sequenced prokaryotic genomes become available through NCBI. As of the second release, ePSORTdb contained over 12,000 entries for bacterial proteins and 800 entries for archaeal proteins; cPSORTdb contained SCL predictions for over 3,700,000 proteins in total. The ePSORTdb data is derived from a manual literature search (using PubMed) as well as Swiss-Prot annotations. The cPSORTdb predictions are generated using the updated PSORTb 3.0 tool. PSORTdb can be accessed through a web interface or via BLAST. The entire database is also available for download under the GNU General Public License. Each term in the database is associated with an identifier from the Gene Ontology in order to allow integration with other bioinformatics resources. As of 2014, PSORTdb is maintained through the laboratory of Fiona Brinkman at Simon Fraser University.

Worked examples

Example 1 — a first encounter with PSORTdb

Start with the simplest possible case. Write down what PSORTdb claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to PSORTdb before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about PSORTdb ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of PSORTdb

In research: PSORTdb appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses PSORTdb in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: PSORTdb is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein databases, Protein targeting, so understanding it makes those chapters shorter.
In everyday life: Look for PSORTdb outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study PSORTdb in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what PSORTdb means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain PSORTdb out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is PSORTdb in simple terms?

PSORTdb is a database of protein subcellular localization (SCL) for bacteria and archaea. It is a member of the PSORT family of bioinformatics tools.

Why does PSORTdb matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study PSORTdb?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on PSORTdb.