EST data

Buetow KH, Edmonson MN, Cassidy AB. Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genet 1999 21 323-325. 

Buetow, K.H., et al., "Reliable Identification of Large Numbers of Candidate SNPs from Public EST Data," Nat. Genet., 21, 323-325 (1999). 

Unlike the situation in nematodes and arthropods, where hundreds of neuropeptides have been elucidated using biochemical, physiological and molecular techniques, flatworm neuropeptide discovery is still in its infancy. This is despite the characterization of the first flat-worm neuropeptide almost 15 years ago (Maule et al., 1991). Progress has been hindered by the inability to obtain large quantities of flatworm neuronal tissues and the absence, until recently, of a significant body of genomic and/or EST data for flatworms. Nevertheless, the available evidence does provide a snapshot of what appear to be the most abundant and widespread flatworm neuropeptides. 

EST data are held in the dbEST database, which maintains its own format and identification number system and is accessible via the NCBI Web server, http // www.nbi.nlm.nih.gov/dbEST/. The sequence data, together with a summary of the dbEST annotation, are also distributed as a subsection of the primary DNA database. The publicly available EST analysis tools fall into three categories ... 

Preliminary EST data fiom this study as well as suppression subtractive hybridization results have identified several promising gene candidates. In addition, we have recently... 

The EST data was mined for candidate polyketide synthases using both the Magic Gene Discovery software (19), and also analyzed by BLAST searches using functionally characterized plant type III polyketide synthase sequences as queries against the EST dataset translated in all possible reading frames. From these analyses, 9 polyketide synthase-like EST s were identified in the root hair EST data set (Table I). Furthermore, candidate EST s were identified for all the other enzymes proposed to be part of the sorgoleone biosynthetic pathway (data not shown). 

With the use of primers that hybridize to the vector sequence, the ends of the cDNA insert are sequenced. Automatic DNA sequencers generate most EST data. If the cDNA has been directionally cloned into the vector, the sequences can be classified as deriving from the 5 or 3 end of the clone. In most cases, both the 5 and 3 sequences are determined, but some EST projects have concentrated only on 5 ESTs to maximize the amount of coding sequence determined. Because the sequence of each EST is generated only once, the sequences may (and often do) contain errors. Contaminating vector, mitochondrial, and bacterial sequences are routinely removed before the EST sequences are deposited into the public databases (Hillier et al., 1996). ESTs in the databases are identified by their clone number as well as their 5 or 3 orientation, if known. 

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