Lecture 31 Bioinformatics & Annotation

Why is the science of bioinformatics necessary? What does a bioinformaticist do?

Bioinformatics is necessary to keep up with the biological data that is produced with modern technology

A bioinformaticist develops databases, gene prediction software, and data mining techniques to interpret biological data.

What is NCBI? What information does it store? What services does it provide?

The National Center of Biotechnology Information (NCBI) creates public databases and conducts research in computational biology.

IT provides access to multiple databases that store many sequences

What is the process of gene annotation? How is comparative genomics important to this process?

Gene annotation involves IDENTIFYING GENE STRUCTURES + ASSIGNING FUNCTIONS

Comparative genomics is important to this process as it BOOSTS ANNOTATION ACCURACY by using evolutionary conservation and cross-species homology.

What is an EST? How can they be used?

An Expressed Sequenced Tag (EST) is a marker associated with an expressed DNA sequence

They can be used in PHYSICAL MAPPING, ORDER AND ASSEMBLE CONTIGS, PREDICT GENE FUNCTION

What is the difference between orthologous and paralogous genes?

Orthologous gene = same ancestral gene, different species, usually same function

Paralogous gene = duplication within one species, may evolve new functions

What is a BLAST search and how can it be used to annotate DNA sequence?

A BLAST search is a tool to compare DNA/Protein sequences against databases

BLAST is used in DNA sequence annotation by matching to known genes, help identify, label, and assign functions to new sequences.

What is positive selection and how is it identified?

Positive selection is when a beneficial mutation increases in frequency within a population.

Positive selection is identified via dn/ds ratio and selective sweeps

What are the two ways to identify positive selection?

The two ways to identify positive selection are:

• dN/dS ratio > 1 = Positive Selection

• dN/dS ratio < 1 = Purifying Selection

• dN/dS ratioo = 1 = normal

• Selective Sweeps

What is the difference between a synonymous and nonsynonymous substitution?

A synonymous substitution WILL NOT change the amino acid that is coded for

A nonsynonymous substitution WILL CHANGE the amino acid that is coded for

What is a selective sweep? What may a large segment of shared SNP haplotypes within a population
indicate?

A selective sweep is a rapid spread of a beneficial allele, dragging linked SNPs with it

Large segments of shared SNP haplotypes = evidence of recent positive selection, or bottleneck event

What is synteny?

A Synteny is a conserved gene order between species

Species 1 - Chr1 = ABCDEFGH

Species 2 - Chr1 = ZYEFGXWV