The Design And Implementation Of Indel Franking Region Database Based On Gridsphere

Bioinformatics is a new area developed with the improvement of biology technology and the accumulation of biology data in the late20th century, and it’s also a subject in which computer tools and technology are utilized for researching the problems and regularities in biology system. Currently, bioinformatics is mainly shown as a combination of molecular biology and information technology, and the key research points are two aspects:Genomics and Proteomics. As the basic substance of life, proteins have been evolving eternally together with the evolution of the nature and all the species, and insertion/deletion (Indel) is one of the most common methods of protein sequence variation. Recent studies showed that protein indel could affect their flanking regions, and this phenomenon is likely to play an important role on protein evolution. Therefore, protein indel have become a key research object in the area of molecular biologyIndel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn) based on Gridsphere Framework is a free Web resource which provides sequence and structure information about indels and their flanking regions in known protein domains. The indels were obtained through the pairwise alignment of homologous structures in Structural Classification of Proteins (SCOP) superfamilies. The IndelFR database contains2,925,017indels with flanking regions extracted from373,402structural alignment pairs of12,573non-redundant domains from1,053superfamilies. All the structural alignment and Indel information were stored in files as the initial form and classified by certain regulations. In order to facilitate retrieval, statistics and analyses, the critical contents were extracted from the files, and then stored in the database. To achieve convenient access by users, Web access is designed for searching in the database, and several different searching methods including basic search, advanced search, ID search, fuzzy search and position search are provided. In addition, a SCOP tree, created according to the information in Structural Classification of Proteins, is contained for browsing the matches and indels in high level. The online indel creation function is also integrated into our platform as a Web application, and there is also a Web page specially for indel dataset downloading.Insertion/deletion (Indel) is the core information in our database, and IndelFR provides access to information about indels and their flanking regions, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity/hydrophobicity, domain information,3D structures, etc. for users. Inde1FR database resource provides lots of facilitation for the research in biology area. The data search and retrieve can be implemented efficiently through our database, valuable statistic information can be obtained, all of which can be utilized for analyzing and summarizing all sorts of biological properties and regularities. Recently, IndelFR has already been used for molecular evolution studies, and it may help to promote future functional studies of indels and their flanking regions.