What is meant by "annotating" the genome? How does annotation differ from assembly?

Answer 1

Annotation differs from assembly in that assembly is about discovering or determining what the sequence is, while annotation is a process used in analyzing the sequence.

Annotation isn't an analytical procedure in and of itself, it merely refers to the process of "marking up" a sequence and attaching some information to a piece of the genome in much the same way one might highlight a passage of interest in a textbook and write a comment into the margins.

If you want to see what annotations look like, the link below shows a sequence entry from GENBANK for human insulin. If one looks at all the lines that begin with the word "REFERENCE" in capital letters those cite scientific articles where scientists have studied that part of the genome and had something to say about it. One can also look at the parts where the words in the left column between the line that starts with the word "FEATURES" and the line which starts with the word "ORIGIN". The parts which start with words like "STS", "CDS", and "polyA_site" all indicate where parts of the sequence correspond to particular biological features or are related to other database entries. These are all forms of annotation. Note that this is not actually genomic sequence, this is RNA sequence, but I picked it because insulin is a familiar gene and it is reasonably compact. Many of the genomic sequences are huge and difficult to navigate. You can find genomic sequences in the database and they'll have similar markings, just many more of them.

Annotation is an important means of conveying knowledge about we collectively understand about different parts of the genome. Scientists collaborate by publishing annotations recording work they've done on different parts of the genome, and read the annotations made by others. One can think of the genome as a bulletin board and as scientists discover how bits of the genome work they record their information as annotations.

This is only the beginning, really. If you want to learn more, a good place to start is the NCBI. Their overview page has a good primer (second link).

Answer 2

Assembly actually compares and lines up the sequences to determine their relation to one another.

Annotating is putting in text descriptors to denote open reading frames, promoters, regulatory sequences etc.