Assessment of Utility of ESTs for Nucleotide Diversity Using Available Assembled Alignments from dbESt, STACK 2.0 and STACK-INDEX

Abstract

Single Nucleotide Polymorphisms (SNPs) in virtual expressed gene fragment alignments represent a potentially signi cant resource for both the detection of non-coding and coding, sequence variations. We have clustered and assembled 767 866 human ESTs into 76 131 alignments localised to speci c tissues [1]. In addition, we have clustered and aligned 300 000 consensus sequences and unclustered ESTs to generate a comprehensive human gene index of over 38 000 unique linked virtual transcripts (STACKINDEX) with associated alignments. The resulting dataset is a potentially rich resource for the detection and characterisation of alternate splicing and polymorphisms. Public access to these data will allow investigators to add functional and scienti c value to the emerging human gene sequences [2]. We have surveyed the dataset and have developed an initial set of criteria for assessment of possible high likelihood SNPs. We have studied the protein p53 as a model for the system.