The partial sequencing of cDNA clones allows the identification of genes in a relatively cost effective manner. In conjunction with the fast evolving information content of public databases it is possible to assign putative functions to a growing number of expressed sequence tags (ESTs).
Currently we are sequencing clones of three different cDNA libraries made from mRNA of cultivar ‘Barke’, which is a high quality spring barley variety used for malting. The libraries were made from etiolated seedlings, roots, and developing caryopsis, respectively. Until now, 8632 EST sequences were generated, mainly from the 5’ end of the corresponding clones. For the assignment of putative functions the EST sequences were used for similarity search against the SwissPirPlus database. We employed the BlastX2--program available at the Heidelberg Unix Sequence Analysis Resources (HUSAR). Searches were performed only with ESTs exceeding a sequence length of 200 bp. Using BlastX2 output a BARLEY ESTBLASTX database managing these search results (n = 7302) was created. The database consists of a search table and the BlastX2 documents in HTMLformat. The search table contains the names of the documents as well as the entire text information of each protein found by BlastX2 search. Using this table a search for a protein (text as any word, several words or partial strings) can be carried out to link all documents containing these search patterns. The text string search is realized by a CGIscript written in C. Finally, a document can be selected to present the entire result of the BlastX2 search and the original sequence for which the search was done. Additionally, a BARLEY ESTSEQ database was created which contains clone designations together with the original EST sequence. Searching for a clone name the corresponding sequence in FASTA format is displayed. For all of the barley ESTs produced a blastable database and a Blast Server were established. The databases as well as the Blast Server are currently accessible as an Intranet solution.
Apart from continued sequencing further goals are the development of new libraries, the advancement of the barley databases and the implementation of bioinformatic tools (e.g. analysis of redundancy, EST clustering).