%0 Journal Article
%T Collembase: a repository for springtail genomics and soil quality assessment
%A Martijn JTN Timmermans
%A Muriel E de Boer
%A Benjamin Nota
%A Tjalf E de Boer
%A Janine MariŁżn
%A Rene M Klein-Lankhorst
%A Nico M van Straalen
%A Dick Roelofs
%J BMC Genomics
%D 2007
%I BioMed Central
%R 10.1186/1471-2164-8-341
%X Collembase is a web-accessible database comprising springtail (F. candida) genomic data. Presently, the database contains information on 8686 ESTs that are assembled into 5952 unique gene objects. Of those gene objects ~40% showed homology to other protein sequences available in GenBank (blastx analysis; non-redundant (nr) database; expect-value < 10-5). Software was applied to infer protein sequences. The putative peptides, which had an average length of 115 amino-acids (ranging between 23 and 440) were annotated with Gene Ontology (GO) terms. In total 1025 peptides (~17% of the gene objects) were assigned at least one GO term (expect-value < 10-25). Within Collembase searches can be conducted based on BLAST and GO annotation, cluster name or using a BLAST server. The system furthermore enables easy sequence retrieval for functional genomic and Quantitative-PCR experiments. Sequences are submitted to GenBank (Accession numbers: EV473060 ¨C EV481745).Collembase http://www.collembase.org webcite is a resource of sequence data on the springtail F. candida. The information within the database will be linked to a custom made microarray, based on the Agilent platform, which can be applied for soil quality testing. In addition, Collembase supplies information that is valuable for related scientific disciplines such as molecular ecology, ecogenomics, molecular evolution and phylogenetics.Organisms are able to maintain homeostasis in changing environments by regulating their metabolic machinery. To accomplish this, organisms continuously have to adjust the expression of their genes. This is particularly evident when environmental challenges drive organisms to the boundaries of their ecological niche and induce stress responses (e.g. [1]). In recent years, significant understanding has been obtained on the signal transduction pathways by which stress affects gene transcription [2]. The question arises whether it is possible to sense aspects of the environment by investigating
%U http://www.biomedcentral.com/1471-2164/8/341