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.
- Find the fugu cosmid sequence entry from GenBank with Accession
and save as GenBank format to MyData in WebLab.
- Find the repeat fragment within the above sequence using dottup in WebLab.
- Retrieve the first fragment (1-13000bp)
and second fragment (13501-25000bp)
of the cosmid sequence using seqret with -sbegin and -send
- Predict the gene structure of the first and second fragments
using GenScan, Softberry and AUGUSTUS, compare the results.
- Retrieve the coding sequence of two genes
as well as their encoded amino acid sequence
from AF164138 with coderet.
- Compare the sequence similarity between MDR2 and MDR3 at the DNA, mRNA and protein level.
- Check the repeat domain within MDR2 and MDR3.
- Predict the potential function of the first gene of fugu cosmid, using different strategies.
- The transporter database for the predicted cytoplasmic membrane transport
protein complement with complete genome sequence.
- Michael Dean, The Human ATP-Binding Cassette (ABC) Transporter Superfamily.
- Liu Y, Cloning and analysis of Takifugu rubripes cosmid sequence.
Peking Medical University, 1998.
- Xu LM, Analysis of the Fugu cosmid sequence. Homework of the ABC course (in Chinese).
A website for the analysis of the Fugu cosmid