Molecular markers play a significant role for livestock improvement in desirable characteristics, such as high milk yields, resistance to disease, high growth rate and other characteristics that will benefit the organism and species in long term. Scientific resources are yet to be developed for water buffalo species which is economically important livestock. Although India has sequenced water buffalo genome but its draft assembly is based on cattle genome Btau 4.0, thus de novo chromosome wise assembly is a major pending issue for global community. In order to cater the urgent need in resolving assembly, mapping issues and biodiversity analysis, first web based relational STR database of water buffalo, BuffSatDb (Buffalo MicroSatellite Database) has been developed using PHP and MySQL. It is simple and systematic web based search for customised retrieval of chromosome wise and genome-wide microsatellites. Search has been enabled based on chromosomes (1-24, X, M and U), motif type (mono, di, tri, tetra, penta and hexa), repeat motif and repeat kind (simple and composite). These searches may be customised by limiting the location on chromosome as well as the number of markers in that range and is a novel approach, not been implemented in any of the existing marker database.
BuffSatDb also fulfils this customized search according to the requirement of researcher, on ranges of GC content, base pair and copy number. This database has been further appended with Primer3 for primer designing of the selected markers with left and right flankings of size upto 500 base pairs, which will enable researcher to select markers of choice at desired interval over the chromosome. A novel add-on for degenerate bases has been incorporated in this database search, where the users are given flexibility to replace degenerate bases with any of the alternative base (A,T,G,C). This feature has been added to resolve the issue of some of the degenerate bases present in current buffalo genome assembly making the primer designing very difficult otherwise.
Citation:
Sarika, Arora Vasu, Iquebal MA, Rai Anil and Kumar Dinesh (2013). In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB. BMC Genomics, 14, 43.
(Published online on 19 January 2013; http://www.biomedcentral.com/1471-2164/14/43/abstract) (Thompson Impact Factor=4.40; NAAS Score= 8.1)
