Expressed Sequence Tags - ESTs
Expressed sequence tags are a cost efficient and rapid way of identifying genes.
We generated 20,000 ESTs for Lumbricus rubellus as part of the EcoWorm consortium, and these are now available in LumbriBASE. They have also been submitted to EMBL/GenBank.
The majority of the EST sequences (~10,000) were picked from a cDNA library produced
from Lumbricus rubellus maintained in a controled environment, including adult and cocoon (larval) sets. The remainder
were from targeted sets of sequences generated from libraries from earthworms exposed
each of the five pollutants used in the project.
The cDNAs were amplified by PCR from bacterial colonies, and ABI 3730 DNA sequencing mahines used to determine the sequences of the cloned transcripts. We filter the sequences for quality, and then assemble them into an estimate of the true set of all transcripts (the transcriptome) using the PartiGene suite of tools. For clustering into putative genes we use CLOBB, and to infer consensus sequences we use the program phrap.
We collect the raw sequences, the assembled consensuses and a variety of annotation information into a database, and provide access to this database through the web.
We have also added EST data from other annelids, including the earthworms Eisenia foetida and Eisenia andrei, and the polychaete Nepenthes (Nereis) virens and the leech Helobdella.
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