Applied Bioinformatics Course

Sequence and function analysis of fugu cosmid sequence

Pufferfish, often known as fugu, or Japanese fugu, or river pig, belongs to the Takifugu genus. There are 25 species in this genus found in salt or fresh water. Genome sequencing of the species of Takifugu rubripes (Dong Fang Hong Qi Tun) was initiated by Sydney Brenner and his colleagues in 1989. The small genome size (~400MB) and similar number of genes make it a good model for comparative genomics. A draft shotgun sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002, and the forth assembly of the genome sequence is available at the Fugu Genome Project website in Singapore.

In 1998, Liu et al. obtained a fugu cosmid sequence of 39757bp (GenBank Accession: AF164138). Five genes were identified with bioinformatics tools in this cosmid: two tandem multidrug resistance (MDR) genes at the 5' followed by three enzymes, (Carnitine octanoyltransferase, RNase P38, and N-myristoyltransferase 2). We use this cosmid sequence as an example for gemomic sequence analysis.

Exercises

References:

A website for the analysis of the Fugu cosmid

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22 November 2017, J Luo, CBI, PKU, Beijing, China