[Design and construction of the platform for comparative genomics].
OBJECTIVE
To design a versatile genome comparison and visualization platform based on browser/server mode supported by a local server.


METHODS
The server of the platform was Apache HTTP server. Perl was used to integrate such genome alignment package and algorithms as MUMmer, LAGAN, and Mauve for different comparison purposes, and the users could submit data and parameters to the platform via the web page. The results of analysis were also returned via the web page.


RESULTS
The platform could handle multiple data input formats, compare complete and draft genome sequence, alignment pair-wise or multi genome of more divergent species, identify regions of high similarity, locate local nucleotide mutations and large-scale recombination, and display the results by visualization interface. Analysis of the homology of 10 new strains of influenza A virus indicated that PB1 gene might evolve from human H3N2 viruses, PB2 and PA genes from avian H3N2 viruses, and HA and NS genes from swine H1N1 viruses. Alignment of Mycobacterium tuberculosis (H37Rv, CDC1551) and Mycobacterium bovis (AF2122/97) genomes revealed that sequence insertion/deletion and duplication were the major source of genomic differences.


CONCLUSIONS
The platform integrate comprehensive resources with a user-friendly interface and intuitive result visualization to facilitate conventional study of comparative genomics.
Institute of Bioinformatics, School of Basic Medical Science, College of Biotechnology, Southern Medical University, Guangzhou 510515, China. liuna520@fimmu.com
Na
N
Liu
Yun-bo
YB
Guo
Xian-he
XH
Sun
Li
L
Ma
Qin-kai
QK
Deng
D001483:Base Sequence; D055028:Comparative Genomic Hybridization / Q000379:methods; D016678:Genome; D023281:Genomics / Q000379:methods*; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000235:genetics; D012984:Software; D014584:User-Computer Interface