Bioinformatic Tools

Question 1

What are the completed genome sequences as of May 2008?

Answer 1

• More than 2000 viruses, defective viruses, and viroids
• 1325 plasmids
• 1373 mitochondria
• 131 chloroplasts
• 109 archaea
• 687 true bacteria
• 23 eukaryotes

Question 2

What are the completed genome sequences as of August 2015?

Answer 2

• 4860 viruses, defective viruses, and viroids
• 5714 plasmids
• 7015 organelles
• 46,988 prokaryotes
• 2384 eukaryotes
• Additional eukaryotic genome sequences are underway

Question 3

What happens to the genome sequences after they are completed?

Answer 3

• The sequences are incorporated into various databases, eg. GenBank and EMBL data library
• Bioinformatics tools are essential for analysing, understanding and mining the sequencing data

Question 4

What is GenBank?

Answer 4

• A Bioinformatics tool
• GenBank is maintained by the National Center for Biotechnology Information (NCBI) in the USA, and is the largest publicly available database of DNA sequences
• Contains about 100 billion bases of sequence, and doubles every 14 months

Question 5

What is GenBank used for?

Answer 5

• Permits identification of genes after a genome has been sequenced -> Annotation
• Compares known sequences in the database with newly sequenced genomic DNA using BLAST (Basic Local Alignment Search Tool)
• Also, as individual genes are sequenced, identified and named, they are deposited into GenBank and given an accession number that can be used for retrieval