Compass of 47,787 cattle ESTs

Comparative Mapping by Annotation and Sequence Similarity (COMPASS) has been demonstrated to be an effective approach for predicting the chromosome location of expressed sequence tags (ESTs) and other sequence-based markers on the basis of comparative mapping information. Herein, we describe the development and use of a computer program to execute the COMPASS strategy en masse. The program was used to identify orthologs and predict map locations of 47,787 cattle ESTs. Among these 47,787 ESTs, 30,097 had significant matches with sequences in the human UniGene database and 21,311 were annotated with human GB4 radiation hybrid mapping data. These sequences are contained within 9,956 and 6,295 individual human UniGene clusters, respectively. The putative human orthologs and predicted cattle chromosome locations of the 21,311 cattle ESTs with GB4 mapping data are provided in this report as a resource for the research community.     

Tandem arrayed ligation of expressed sequence tags (TALEST): a new method for generating global gene expression profiles.

We have developed a new and simple method for quantitatively analyzing global gene expression profiles from cells or tissues. The process, called TALEST, or tandem arrayed ligation of expressed sequence tags, employs an oligonucleotide adapter containing a type IIs restriction enzyme site to facilitate the generation of short (16 bp) ESTs of fixed position in the mRNA. These ESTs are flanked by GC-clamped punctuation sequences which render them resistant to thermal denaturation, allowing their concatenation into long arrays and subsequent recognition and analysis by high-throughput DNA sequencing. A major advantage of the TALEST technique is the avoidance of PCR in all stages of the process and hence the attendant sequence-specific amplification biases that are inherent in other gene expression profiling methods such as SAGE, Differential Display, AFLP, etc. which rely on PCR.