We are updating the database "NEXTDB" to integrate all the information of ESTs, gene expression patterns and gene functions of C.elegans which are being produced and analyzed in this laboratory. In addition to the EST sequences from the previous 130,000 cDNA clones (lambda ZAP clones and oligo-cap clones) which were classified into 14,000 unique transcripts, this time we obtained ESTs from new full-length cDNA clones made by the V-capping method. This method generates cDNA clones of more full length and less mutation. We classified tag sequences of the 100,000 clones and found additional 1,000 unique transcripts, as well as 6,500 kinds which were also found in the previous clones. Then they were compared to genome sequences by use of BLASTN and predicted structures of genes strictly. BLASTX searches and motif searches by HMM are also done to predict functions of CDSs. As to whole mount in-situ hybridization of 11,000 genes, we continue to annotate their developmental stages and expression patterns. The images and their description of RNAi phenotypes of 900 genes and antibody staining images which showed localization of 660 proteins were also stored in the database. All the images and annotations are arranged based on the corresponding cDNA clones. All the data are integrated with the genome map based on WWW, and the information of maps and their relations are displayed visually. The latest version is opened through the following URL.
http://nematode.lab.nig.ac.jp We also have started EST/genome analysis of other nematode Diploscapter coronatus in collaboration with Dr. Einhard Schierenberg at Univ. of Koeln, since we are interested with its different cell cleavage and arrangement pattern to gastrulation stage. EST sequencing and preliminary assembling of low-coverage whole genome shotgun sequencing are in progress. All the results were also incorporated to NEXTDB.