Abstract: BACKGROUND AND AIM: In order to provide further support for the experimental verification and functional exploration of 48 DNA sequences related to esophageal carcinoma found in our lab, these sequences were investigated systematically using bioinformatics methods such as silicon cloning and BLAST search tool. MATERIALS AND METHODS: A local database including the 48 sequences was constructed by the BioEdit software; the 48 DNA sequences coding unknown genes were extended by the method of silicon cloning; the potential ncRNAs, located in the introns, the upstream and downstream of intergenic regions of the above 48 DNA sequences, were analyzed by BLAST tool. RESULTS: The sequences coding unknown genes were extended to more than 190 bp on average using silicon cloning. Some sequence segments with high similarity to the known noncoding RNA(ncRNAs) were found in the intronic or intergenic regions. CONCLUSION: Some esophageal carcinoma related genes can be extended obviously by the method of silicon cloning,some sequences with high similarity to known ncRNAs were found in the chromosome region where the esophageal carcinoma related genes are located. The information gives us potential clues that these ncRNAs maybe participate in the development process of esophageal carcinoma, and the functions of these ncRNAs needs further study.

Key words: bioinformatics, sequence analysis, noncoding RNA, silicon cloning