ProbCons

Key takeaways

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

Reference excerpt

In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advantage in accuracy over similar tools, including Clustal and MAFFT.

Algorithm The following describes the basic outline of the ProbCons algorithm.

Step 1: Reliability of an alignment edge For every pair of sequences compute the probability that letters x i {\displaystyle x_{i}} and y i {\displaystyle y_{i}} are paired in a ∗ {\displaystyle a^{*}} an alignment that is generated by the model.

P ( x i ∼ y i | x , y ) = d e f Pr [ x i ∼ y i in some a | x , y ] = ∑ alignment a with x i − y i Pr [ a | x , y ] = ∑ alignment a 1 { x i − y i ∈ a } Pr [ a | x , y ] {\displaystyle {\begin{aligned}P(x_{i}\sim y_{i}|x,y)\ {\overset {\underset {\mathrm {def} }{}}{=}}&\ \Pr[x_{i}\sim y_{i}{\text{ in some }}a|x,y]\\[8pt]=&\ \sum _{{\text{alignment }}a \atop {{\text{with }}x_{i}-y_{i}}}\Pr[a|x,y]\\[2pt]=&\ \sum _{{\text{alignment }}a}\mathbf {1} \{x_{i}-y_{i}\in a\}\Pr[a|x,y]\end{aligned}}}

(Where 1 { x i ∼ y i ∈ a } {\displaystyle \mathbf {1} \{x_{i}\sim y_{i}\in a\}} is equal to 1 if x i {\displaystyle x_{i}} and y i {\displaystyle y_{i}} are in the alignment and 0 otherwise.)

Step 2: Maximum expected accuracy The accuracy of an alignment a ∗ {\displaystyle a^{*}} with respect to another alignment a {\displaystyle a} is defined as the number of common aligned pairs divided by the length of the shorter sequence. Calculate expected accuracy of each sequence:

… excerpt ends here. Continue reading the full article.

Worked examples

Example 1 — a first encounter with ProbCons

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

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

How to study ProbCons in 20 minutes

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

Frequently asked questions

What is ProbCons in simple terms?

In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advant…

Why does ProbCons 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 ProbCons?

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 ProbCons.