Answer to Question #154921 in Bioinformatics for vaibhav

Question

(a) What is a sequence pattern? Explain the use of patterns for functional annotation.

(b) What are True positive, True negative, False positive, and False-negative in the context of pattern searches in protein sequences? How to obtain sequence patterns?

Answer 1

(a) A sequence pattern is a procedure or rule that is followed to predict outcomes, for example a set of numbers arranged in a particular order, an arrangement called a sequence. In Bioinformatics, sequence analysis is the subjecting of biomolecules to analytical methods so as to predict their features, functions, structure, and or evolution. For example, binding sites of enzymes that consist of fewer amino acids can be used a s patterns to recognize the mentioned features. Patterns are build to identify these regions in multiple sequence alignments, the pattern of conservation within the sequence is then modeled as a regular expression.

Functional annotation is the process of attaching biological information to sequences of biomolecules e.g. genes by use of sequence alignment tool BLAST to find similarities and the annotating the genes based on that.

(b) True positive is an outcome where the model correctly predicts the positive class, while true negative is one where the model correctly predicts a negative class.

False positive is an outcome where the model incorrectly predicts the positive class while a false negative is where the model incorrectly predicts the negative class

Patterns usually correspond to functionally or structurally important elements in proteins or DNA sequences. For example, binding sites of enzymes that consist of fewer amino acids can be used a s patterns to recognize the mentioned features. Patterns are build to identify these regions in multiple sequence alignments, the pattern of conservation within the sequence is then modeled as a regular expression.