Snake Transcriptomics

Here we provide easy access to our molecular data from the Western terrestrial garter snake (Thamnophis elegans) and tools for using the data. We provide a Blast server (ViroBlast, Deng et al. 2007) to search specifically against our assembled transcriptomes: (1) a multiple-tissue transcriptome using 454 (pyrosequencing data) as described in Schwartz et al., 2010; and (2) a liver transcriptome using Illumina data from 12 females from a heat stress experiment as described in Schwartz and Bronikowski 2012. The Transcriptome Browser allows users to view our 454 assembly (Schwartz et al., 2010) mapped against the anolis lizard draft genome (anoCar1.0). The Transcriptome Browser and access to the assembled data is served by Indiana University Center for Genomics and Bioinformatics. We also provide a 2007 excel (.xlsx) file containing the annotated data for the 454 transcriptome with hyperlinks to their Blast hits and information on ORF predictions, variants, etc. Finally, both of the transcriptomes can be downloaded as fasta files. The raw data has been archived in NCBI SRA: 454 dataset (SRA010134), the Illumina dataset (SRA052923)

EcoDatabases

These databases contain long-term ecological and life-history data for particular species. They have been developed in collaboration with the BCBlab

References

 •  Schwartz TS, Tae H, Yang Y, Mocktalis K, Van Hemert JL, Proulx S, Choi J-H, Bronikowski AM: 2010. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics 11:694

 •  Schwartz TS, Bronikowski AM: 2012. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes. Molecular Ecology In Press

 •  Deng W, Nickle DC, Learn GH, Maust B, Mullins JI: ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 2007, 23(17):2334-2336.