Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usua...Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http：//moodle.fct.unl.pt/course/view.php？id=2079 or https：//sourceforge.net/projects/bidiblast/ under the GNU GPL license.展开更多
Many countries are promoting biofuels as a substitute for scarce oil. This paper develops a dynamic model of land allocation between food and energy and shows how the model can be calibrated using standard optimizatio...Many countries are promoting biofuels as a substitute for scarce oil. This paper develops a dynamic model of land allocation between food and energy and shows how the model can be calibrated using standard optimization techniques. Some possible implications of the trade-offs between food and energy are discussed. Specifically, we show that the effect of mandates is mainly felt through increased land conversion, which increases indirect carbon emissions Crude oil prices do not decrease significantly because of leakages.展开更多
文摘Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http：//moodle.fct.unl.pt/course/view.php？id=2079 or https：//sourceforge.net/projects/bidiblast/ under the GNU GPL license.
文摘Many countries are promoting biofuels as a substitute for scarce oil. This paper develops a dynamic model of land allocation between food and energy and shows how the model can be calibrated using standard optimization techniques. Some possible implications of the trade-offs between food and energy are discussed. Specifically, we show that the effect of mandates is mainly felt through increased land conversion, which increases indirect carbon emissions Crude oil prices do not decrease significantly because of leakages.
