PLATCOM: Current Status and Plan for the Next Stages [chapter]

Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim
2005 Lecture Notes in Computer Science  
We have been developing a system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational tools. PLATCOM is built on internal databases such as GenBank, COG, KEGG, and Pairwise Comparison Database (PCDB) that contains all pairwise comparisons (97,034 entries) of protein sequence files (.faa) and whole genome sequence files (.fna) of 312 replicons. PCDB is designed to incorporate new
more » ... enomes automatically, so that PLAT-COM can evolve as new genomes become available. PLATCOM is available at http://platcom.informatics.indiana.edu. The design goal of PLATCOM is to provide a flexible environment for comparison of genomes from the "sequence analysis perspective." Comparison of multiple genomes is a challenging task since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool. To alleviate such problem, we borrowed techniques from existing systems, and we have also developed and incorporated high performance sequence data mining tools such as sequence clustering and neighborhood prediction. High performance data mining tools have been useful in integrating separate system modules by gluing them together on the biological sequence level. PLATCOM is designed to evolve through three development stages. Its first stage is complete: the underlying architecture and individual system modules. We share our experience in designing and implementing PLATCOM and then discuss our current design strategies that have been refined from our experience after the completion of the first implementation stage.
doi:10.1007/11530084_27 fatcat:erlumy5g6vfltp73qn6ojzagnu