Genome Analysis

Some important repositories of genomic information:

• TIGR (Genomes and progress of new sequencing projects)

• Genome Information Broker in Japan

• NCBI genomes (viruses, bacteria, eukaryotes)

• Nature genomics page

• GenomeNet in Japan(Bibliography, metabolic pathways, genomes. Very complete)

• Sanger Center (Human data)

• Colibri (Escherichia coli repository)

Genome Analysis systems:

DANTE: Viral genomes analysis.

• GeneQuiz: GeneQuiz derives functional annotation for protein sequences and provides supporting evidence, including family alignments.

 
• Two examples of Genequiz analysis results:  (Example 1) (Example 2)

Methabolic Pathways Databases:

• MGDB, Microbial Genome Database for Comparative Analysis . MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of  MBGD is to facilitate comparative genomics from various points of view such as orthologue identification, paralogue clustering, motif analysis and gene order comparison.

• Exercise: At the main MGDB page, enter the name of a gene :"FtsA" (this gene is widely distributed in bacteria; it belongs to a cluster of proteins related to bacterial division processes) and press Exec. The RESULT is a list of homologous genes to FtsA in different organisms. Clicking on each gene name, a new page containing gene and gene cluster information is provided [EXAMPLE].

• KEGG, Kyoto Encyclopedia of Genes and Genomes, is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects.

• Exercise 1: At the main KEGG page, select "Open KEGG" and then "Identify gene clusters in two genomes -point 2.2-" . Select 'Escherichia coli' and 'Rickettsia prowazekii' as the two organisms. After pressing "Exec", a page showing some gene clusters appears. Following the link "Gene Clusters: 1 - 10" , the third cluster shows a pair of non homologous genes (b0083-RP568 [HERE]). The first one is the protein ftsL (related to cellular division). The second one is unknown. This coincidence (and some other comparisons with organisms as H. influenzae or  B. subtilis) suggests that  RP568 could act as ftsL in  Rickettsia prowazekii.
• Exercise 2: At the point 1.1 press "Metabolic pathways" and then "Glycolysis". At the [MAP], select Pyrococcus abysii and press "Exec" (The result is also HERE). This organism doesn't possess the enzyme 5.4.2.1 (Phosphoglycerate mutase). The gene for this enzyme hasn't been identified in this organism, but it must exist. So, the gene have to be searched into the entire genome of  Pyrococcus abysii .