ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional biological experimental techniques. Protein function prediction has been a long standing challenge to fill the gap between the huge amount of protein sequences and the known function. In this paper, we propose a novel method to convert the protein function problem into a language translation problem by the new proposed protein sequence language "ProLan" to the protein function language "GOLan", and build a neural machine translation model based on recurrent neural networks to translate "ProLan" language to "GOLan" language. We blindly tested our method by attending the latest third Critical Assessment of Function Annotation (CAFA 3) in 2016, and also evaluate the performance of our methods on selected proteins whose function was released after CAFA competition. The good performance on the training and testing datasets demonstrates that our new proposed method is a promising direction for protein function prediction. In summary, we first time propose a method which converts the protein function prediction problem to a language translation problem and applies a neural machine translation model for protein function prediction.Comment: 13 pages, 5 figure

Public Perception of Invasive Plant Species: Assessing the impact of workshop activities to promote young students’ awareness

Invasive species are one of the main threats to biodiversity worldwide. Even though they are identified and recognized as such by the Portuguese law, the majority of the population is not yet aware of this problem. Aiming to increase awareness about biological invasions among young students, a workshop on Invasive Plant Species was organized at the Botanical Museum of the University of Coimbra. A total of 170 teenager students from five schools participated in the workshop. Three activities were prepared, focusing on: (1) identification of invasive plants, (2) competition between native and invasive plants and (3) control of invasive plants. One year later, questionnaires were sent to the participants, aiming to appraise workshop effectiveness, and this questionnaire revealed that these students know more about invasive plant species than a comparable group of students that did not participate in the workshop. The results clearly showed that practical informal education activities may be effective in raising public awareness. Questionnaires were essential to evaluate the knowledge acquired and retained by the students during the workshop.This workshop was supported by FCT-MCTES (Portuguese Foundation for Science and Technology) and European fund FEDER, project INVADER II—Invasion processes, control and restoration of coastal ecosystems invaded by Acacia longifolia—PPCDT/AMB/61387/ 2004