EST-PAC HPC - a web portal for high-throughput EST annotation and protein sequence prediction

Expressed Sequence Tags (ESTs) are short DNA sequences generated by sequencing the transcribed cDNAs coming from a gene expression. They can provide significant functional, structural and evolutionary information and thus are a primary resource for gene discovery. EST annotation basically refers to the analysis of unknown ESTs that can be performed by database similarity search for possible identities and database search for functional prediction of translation products. Such kind of annotation typically consists of a series of repetitive tasks which should be automated, and be customizable and amenable to using distributed computing resources. Furthermore, processing of EST data should be done efficiently using a high performance computing platform. In this paper, we describe an EST annotator, EST-PACHPC, which has been developed for harnessing HPC resources potentially from Grid and Cloud systems for high throughput EST annotations. The performance analysis of EST-PACHPC has shown that it provides substantial performance gain in EST annotation.

When surfacers do not dive : multiple significance of extended surface times in marine turtles

Marine turtles spend more than 90% of their life underwater and have been termed surfacers as opposed to divers. Nonetheless turtles have been reported occasionally to float motionless at the surface but the reasons for this behaviour are not clear. We investigated the location, timing and duration of extended surface times (ESTs) in 10 free-ranging loggerhead turtles (Caretta caretta) and the possible relationship to water temperature and diving activity recorded via satellite relay data loggers for 101–450 days. For one turtle that dived only in offshore areas, ESTs contributed 12% of the time whereas for the other turtles ESTs contributed 0.4–1.8% of the time. ESTs lasted on average 90 min but were mostly infrequent and irregular, excluding the involvement of a fundamental regulatory function. However, 82% of the ESTs occurred during daylight, mostly around noon, suggesting a dependence on solar radiation. For three turtles, there was an appreciable (7°C to 10.5°C) temperature decrease with depth for dives during periods when ESTs occurred frequently, suggesting a re-warming function of EST to compensate for decreased body temperatures, possibly to enhance digestive efficiency. A positive correlation between body mass and EST duration supported this explanation. By contrast, night-active turtles that exceeded their calculated aerobic dive limits in 7.6–16% of the dives engaged in nocturnal ESTs, probably for lactate clearance. This is the first evidence that loggerhead turtles may refrain from diving for at least two reasons, either to absorb solar radiation or to recover from anaerobic activity.