( y belong to one gene. They can also gro...)The GeneZoo or the GeneJungle?

y belong to one gene. They can also group exons into one gene when they really belong to two or more genes. Thus the importance of high quality cDNA collections is rising once again. cDNAs are an excellent way of confirming gene structure, and Stratagene has a highly unique, well-characterized collection of 1.7 Kb average length human cDNA clones. Approximately 40% of Stratagenes cDNA clusters cannot be found in UniGene, and based on our initial in-house analysis of known sequences about 50% of Stratagenes clones contain full-length open reading frames which corresponds to our predicted estimate for the collection.

Inherent Problems with Clustering ESTs

ESTs (Expressed Sequence Tags) are DNA sequences derived from sequencing the 5 and/or 3 termini of cDNA inserts using vector-specific sequencing primers. Each EST sequence is typically 300 to 600 nucleotides in length. The dbEST database currently contains about 2.1 million human ESTs. UniGene is an attempt to reduce these sequences to a non-redundant set of gene-oriented sequence clusters. In theory there should be one cluster for each underlying gene. Build #116 of UniGene (July 3, 2000) has produced 81,967 unique clusters. However UniGene is plagued with many artifacts. The ESTs found in dbEST have come from many different sources, with widely varying degrees of sequence quality. The quality of the cDNA libraries from which these ESTs were derived is variable. Sometimes two cDNAs can be fused together in one vector. This creates UniGene artifacts whereby two unrelated cDNAs are placed into the same UniGene cluster. Genomic DNA contamination is common, as well as are products resulting from aberrant transcription and termination. Splice variants are of course common, and it is difficult for the UniGene clustering algorithms to differentiate splice variants from different gen
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