News

cDNA library

In order to generate an EST resource for the mink genome, a normalized cDNA library from a six months old mink brain has been produced.

Sequence analysis of approximately 3000 randomly picked clones revealed that 1730 were unique. The resulting sequences have an average of 830 bp ranging from 55 bp to 1061 bp.

BLASTN results were analyzed and 1253 of the 1730 unique ESTs (71%) have significant similarity (BLAST matches with a score > 100) to known genes in the public GenBank database. Subsequently, a Pearl script was used to extract the hits results for each EST names and to generate putative name for each clone. The ESTs sequences that were “clean” and overlapped minimum 50 bp with almost perfect identity were subsequently assembled in consensus sequences. To identify homology to known genes, BLAST searches were performed against the NCBI RefSeq sequences uploaded into our Linux managed database using score values cutoffs of 100. For more than 90% of them, the e value was at least 0. Each clone was annotated with a title based on the best BLAST results of the clone sequence and the respective contig sequence. Homology at a significance level (score of 100) was labeled “similar to” and the rest have got a generic name “clone number derived from mink brain cDNA”. Sequence information of all ESTs has been submitted to GenBank (Accession numbers ES609118 through ES610847).

Updated 21.05.2008