The HAMAP project

Table of contents

The HAMAP project

Going from microbial genomes to microbial proteomes

Microbial genome sequencing

Complete genomes of human pathogens

From a genome to a proteome

Some preliminary assumptions

A typical day in the life of a modern bioinformatician

What can we do in SWISS-PROT to cope with all these microbial genome sequences?

HAMAP

Access to proteomes of complete microbial genomes

Categorization of the annotations tasks for a complete microbial proteome

General flow chart

HAMAP flow chart 1

HAMAP flow chart 2

Automatic annotation of microbial proteins with “0 neighbor”

An example: Before automatic annotation (1)

An Example: After automatic annotation (2)

Inteins annotation

Pre-annotation of proteins belonging to large/complex families

Automatic annotation of proteins belonging to specified families (1)

Automatic annotation of proteins belonging to specified families (2)

An excerpt of an entry in the microbial organism rule file (1)

An excerpt of an entry in the microbial organism rule file (2)

An example of a family rule (1)

An example of a family rule (2)

An example of a family rule (3)

An example of a family rule (4)

Examples of checking rules

Additional clean up tasks

Integrating high throughput proteomics information

The case of the Escherichia coli proteome

Extension of HAMAP

The HAMAP project participants

Author:

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