Plant & Animal Genome IX Conference Plant & Animal Genome IX Conference
Poster: Databases
P9a_19.html
The generation of single pass, partial sequences from cDNA clones (ESTs) has become an extensively used strategy for gene discovery and mapping in a wide range of plant organisms. In order to create an EST collection for barley, cDNA libraries from three tissues were analysed. Until now sequence information from 7,500 clones (13,000 sequences) was entered into the database. Apart from the sequence information B-EST (http://pgrc.ipk-gatersleben.de/) contains the results of database searches which are updated periodically, and information about EST clusters. For the assignment of putative functions the trimmed ESTs (without vector sequences and low quality sequence ends) were used for BlastX2 and BlastN2 similarity searches against the non-redundant protein- and nucleotide sequence databases of the NCBI (available at HUSAR). The database containing the ESTs and the Blast-results was built up using the mySQL DBMS. With the aim to identify an UniGene set of barley the ESTs were analysed for redundancy and cluster formation. Using the STACK_PACK software package consisting of CrossMatch for vector masking, d2_Cluster for clustering, PHRAP for assembling and a post-clustering step more than 4000 Tentative UniGenes were identified in the present set of clones. Using a online request form, researchers may access data of the IPK-EST sequencing effort.