Lecture 1 - Databases

What is the convention for showing DNA?

The orientation is determined by which end is 5’ and which is 3’, either strand can be the template (antiparallel), but the convention is to show the non-template strand as it resembles RNA

What is the convention for showing proteins?

They have polarity with an N terminus presented on the right and the C terminus on the left. Amino acids are given a single letter code

What is a file type?

A software package developed for the analysis of DNA and protein sequences, typically they only accept a specific file format

What does > signify?

It tells the computer that the following code is a title

What is an accession no.?

A unique code that applies to a sequence

How is a sequence started in GenBank?

‘LOCUS’, literally location or a line containing ‘ORIGIN’ and the end of the sequence is marked by ‘//’

What is a primary database?

Hold the experimentally determined nucleotide sequence information, together with the protein sequences inferred from the conceptual translation of these nucleotide sequences eg GenBank

What is a secondary database?

Contain the results of analysis of the sequences held in primary databases. Many secondary protein databases are the result of looking for features that relate different proteins.