biology

TIGRFAMs

TIGRFAMs 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 TIGRFAMs rather than just read about it. In short: TIGRFAMs is a database of protein families designed to support manual and automated genome annotation. Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment.

Key takeaways

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

Reference excerpt

TIGRFAMs is a database of protein families designed to support manual and automated genome annotation. Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment. Sequences that score above the defined cutoffs of a given TIGRFAMs HMM are assigned to that protein family and may be assigned the corresponding annotations. Most models describe protein families found in Bacteria and Archaea. Like Pfam, TIGRFAMs uses the HMMER package written by Sean Eddy.

History TIGRFAMs was produced originally at The Institute for Genomic Research (TIGR) and its successor, J. Craig Venter Institute (JCVI), but it moved in April 2018 to the National Center for Biotechnology Information (NCBI). TIGRFAMs remains a member database in InterPro. The last version from JCVI, release 15.0, contained 4488 models. TIGRFAMs now continues at NCBI as part of a larger collection of HMMs, called NCBIFAMs, used in its RefSeq and PGAP genome annotation pipelines. Active curation and revision of TIGRFAMs models continues at NCBI, but the creation of TIGRFAMs models per se has ended, as newly constructed HMMs from the RefSeq group receive different designations when added to NCBIFAMs.

References

External links nih.gov - TIGRFAMs home page https://www.ebi.ac.uk/interpro/ - InterPro home page nih.gov - TIGRFAMs text search at NCBI nih.gov - FTP site with most recent versions of TIGRFAMs, as part of a larger collection

Worked examples

Example 1 — a first encounter with TIGRFAMs

Start with the simplest possible case. Write down what TIGRFAMs 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 TIGRFAMs 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 TIGRFAMs 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 TIGRFAMs

In research: TIGRFAMs 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 TIGRFAMs 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: TIGRFAMs is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics stubs, Biological databases, so understanding it makes those chapters shorter.
In everyday life: Look for TIGRFAMs 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.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study TIGRFAMs in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TIGRFAMs 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 TIGRFAMs out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TIGRFAMs in simple terms?

Why does TIGRFAMs 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 TIGRFAMs?

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 TIGRFAMs.