7 Computational Methods and Tools Free Online FlashCards

What is an algorithm?

An algorithm is a defined procedure for solving a problem; its usefulness depends on the quality of its answer and the resources it requires.

How does dynamic programming find an alignment?

It fills a table with optimal scores for smaller sequence prefixes, then traces through the table to recover an alignment.

How do global and local alignment differ?

Global alignment compares sequences across their full lengths; local alignment finds their most similar subsections.

Which classic methods perform global and local alignment?

Needleman–Wunsch is a classic global alignment method; Smith–Waterman is a classic local alignment method.

How does BLAST search sequence databases?

BLAST finds short candidate matches, extends promising ones, and reports alignments with scores and statistical estimates. It is a heuristic, not an exhaustive calculation of every possible alignment.

What does a BLAST E-value estimate?

An E-value estimates how many matches scoring at least as well as the observed match are expected by chance in a search of that database size. A lower value generally gives stronger evidence against a chance match.

How can a k-mer index speed up sequence searches?

A k-mer index stores locations of short sequence words, helping searches such as read mapping avoid repeatedly scanning every position.

How can graphs support genome assembly?

Overlapping reads can be represented as paths or edges in a graph; algorithms use the graph to infer a sequence or set of contigs consistent with the read evidence.

What does a p-value mean?

A p-value is the probability, assuming the null hypothesis and statistical model are true, of observing a result at least as extreme as the one obtained.

What does an FDR threshold control?

The Benjamini–Hochberg false-discovery-rate method adjusts interpretation across a set of tests. An FDR threshold controls the expected proportion of false discoveries among results called significant under the method’s assumptions.

What base-calling error probabilities correspond to Q20 and Q30?

The Phred scale relates score and estimated base-calling error probability by $Q = -10\log_{10}(P)$. Thus Q20 corresponds to an estimated 1% error probability, and Q30 to 0.1%.

What do workflow managers provide for bioinformatics analyses?

Workflow managers specify analysis steps, dependencies, inputs, and outputs. They help automate repeatable runs and scale analyses across computers or platforms.