In these lectures, we will build on the 2GEN lectures and previous lectures in the 3GNO lecture series to examine some applications of bioinformatics to functional genomics. At the end of the lectures you should:

\u2022Be able to describe how bioinformatics is used as a tool to functionally annotate genomes
\u2022 Be able to discuss issues in assigning biological function
\u2022 Recognise novel bioinformatics techniques currently being developed for comparative and

In second year lectures, we considered how sequence similarity searching (with programs such as BLAST and FASTA) can find homologous genes and proteins, based on common patterns in their primary sequences. The function of the unknown gene or protein sequence is inferred from the function of the database match based on the hypothesis that the proteins share aco mmo n

"twilight zone" of c.25% pairwise sequence identity beyond which no statistical significance can be assigned to a match, even when the proteins do share a common ancestral gene. However, many genes in the yeast genome where seen to fall into this category - roughly 2000 so-called

A schematic of the process involved in annotating a genome sequence is shown above. We hope we can find many orthologous genes from other genomes whose function is well characterised.

Unknown
(new) query
sequence

Unknown
(new) query
sequence

Align all \u201chits\u201d
with score better
than threshold

Align all \u201chits\u201d
with score better
than threshold

BLAST profile
against
database

BLAST profile
against
database