Searching the expressed sequence tag (EST) databases: Panning for genes

Searching the Expressed Sequence Tag (EST) Databases: Panning for Genes

The genomes of living organisms contain many elements, including genes coding for proteins. The portions of the genes expressed as mature mRNA, collectively known as the transcriptome, represent only a small part of the genome. The expressed sequence tag (EST) databases contain an increasingly large part of the transcriptome of many species. For this reason, these databases are probably the mos...

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries.

Expressed sequence tags (ESTs) are randomly sequenced cDNA clones. Currently, nearly 3 million human and 2 million mouse ESTs provide valuable resources that enable researchers to investigate the products of gene expression. The EST databases have proven to be useful tools for detecting homologous genes, for exon mapping, revealing differential splicing, etc. With the increasing availability of...

Discovering Fragrance Biosynthesis Genes from Vanda Mimi Palmer Using the Expressed Sequence Tag (EST) Approach

A hitchhiker's guide to expressed sequence tag (EST) analysis

Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as functiona...

A Parallel Expressed Sequence Tag (EST) Clustering Program

This paper describes the UIcluster software tool, which partitions Expressed Sequence Tag (EST) sequences and other genetic sequences into “clusters” based on sequence similarity. Ideally, each cluster will contain sequences that all represent the same gene. If a näıve approach such as anNxN comparison (N is the number of sequences input) is taken, the problem is only feasible for very small da...