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Aiptasia pallida

Welcome to AiptasiaBase!

AiptasiaBase is a database of annotated ESTs from the symbiotic sea anemone Aiptasia pallida.

To get started: go to the log in page and use the provided name and password to log on to the main search page. Select the version of the EST assembly that you would like to browse.

     AiptasiaBase_v1 is the assembly described in Sunagawa et al 2009

      AiptasiaBase_v2 is the most current; includes ESTs from 454 run.

From the main search page, you can use the blast function, link to annotations, download sequences, or perform other search functions.

EST Assembly: The ESTs were generated from a large-insert cDNA library prepared from a clonal line of symbiotic anemones living in standard culture conditions. Each large-insert plasmid clone was sequenced from both the 5' and 3'ends. The ESTs were then assembled into a set of contiguous sequences (Contigs) and single ESTs (singletons). Please note that in most cases, there are two separate contigs for each gene, one which represents the 5' end and one which represents the 3' end.

Annotation: The contigs and singletons were annotated using BLAST, GO, and KEGG (the KEGG annotations also list our predictions for whether the genes originate from the host or symbiont genomes). Potential single nucleotide polymorphisms and simple repeats are also annotated.

Also, check out the development of AiptasiaWiki, a wiki platform for creating custom bioinformatics pipelines.

AiptasiaBase Citations:

Sunagawa, S., Wilson, E.C., Thaler, M., Smith, M.L., Caruso, C., Pringle, J.R., Weis, V.M., Medina, M., and J.A. Schwarz. 2009. Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. BMC Genomics 2009, 10:258.

Wood-Charlson, E. and V.M. Weis. 2009. The diversity of C-type lectins in the genome of a basal metazoan, Nematostella vectensis. Dev Comp Immunol 33: 881-889.

Sunagawa, S., DeSalvo, M., Voolstra, C. Reyes-Bermudez, A., and M. Medina. 2009. Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals. PLoS One, 4(3):e4865.