Development of SRS. php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Abundance and diversity of resistance genes in the sugarcane transcriptome revealed by in silico analysis

Resistance genes (R-genes) are responsible for the first interaction of the plant with pathogens being responsible for the activation (or not) of the defense response. Despite their importance and abundance, no tools for their automatic annotation are available yet. The present study analyzed R-genes in the sugarcane expressed sequence tags database which includes 26 libraries of different tissues and development stages comprising 237,954 expressed sequence tags. A new annotation routine was used in order to avoid redundancies and overestimation of R-gene number, common mistakes in previous evaluations. After in silico screening, 280 R-genes were identified, with 196 bearing the complete domains expected. Regarding the alignments, most of the sugarcane’s clusters yielded best matches with proteins from Oryza sativa, probably due to the prevalence of sequences of this monocot in data banks. All R-gene classes were found except the subclass LRR-NBS-TIR (leucine-rich repeats, nucleotide-binding site, including Toll interleukin-1 receptors), with prevalence of the kinase (Pto-like) class. R-genes were expressed in all libraries, but flowers, transition root to shoot, and roots were the most representative, suggesting that in sugarcane the expression of R-genes in non-induced conditions prevails in these tissues. In leaves, only low level of expression was found for some gene classes, while others were completely absent. A high allelic diversity was found in all classes of R-genes, sometimes showing best alignments with dicotyledons, despite the great number of genes from rice, maize and other grasses deposited in data banks. The results and future possibilities regarding R-genes in sugarcane research and breeding are further discussed.