In this proposal we also will take advantage of mapped cDNA contigs from AZD9291 lung cancer various garter snake tissues (10 tissue types will be selected) to improve assembly contiguity and accuracy, strengthening the genic component of this assembly. Each of these metrics reveals something unique about the assembly and defines overall the strengths and weaknesses of an assembly. During our manual review of the assembly errors these are corrected when possible. We will screen the genome assembly for contamination, and then submit the de-contaminated sequence to the WGS division of Genbank for an independent contamination analysis. A Genbank analysis typically will reveal small amounts of additional contamination due to BLAST parameter differences and the use of updated databases that are removed followed by resubmission to Genbank.
The final assembly will be uploaded to multiple online databases and genome browsers, including Ensembl , the University of California Santa Cruz  and NCBI for public queries. Gene annotation First-pass gene prediction will use a modified Ensembl pipeline , for evidence-supported gene model building and model merging. Uniprot protein sequences from several species will be used sequentially as seeds for coding sequence prediction. In addition, cDNA sequences from the garter snake will be aligned and used to find genes and add UTR information. The consortium will select 10 diverse tissues for Illumina RNA sequencing. A portion of the Ensembl mandate is to work directly with genome sequencing projects, and use custom-curated data sets (such as EST sequences and specific Uniprotdata sets) to enable annotation.
Should other groups provide gene sets with independent gene prediction algorithms, the Ensembl group can easily merge these gene predictions into a unique set of predicted genes. We have successfully followed this paradigm for the many other species. Promise of garter snakes for ecological and comparative genomics Promise as a model system in physiology Reptiles possess many adaptations related to mortality selection that suggest their usefulness in studies that link morphological and physiological evolution. Snakes in particular, have evolved venom, limblessness, extended metabolic shut-down�C including both hibernation and estivation, starvation resistance, heat tolerance and hypoxia resistance. Furthermore, although species possess species-specific lifespans, little physiological decline occurs with advancing age in snakes until near the end of their lifespans. Thus, some Carfilzomib snakes may indeed exhibit the phenomenon known as negligible senescence  �C the lack of age-related deterioration.