Testing statistical significance scores of sequence comparison methods with structure similarity

BACKGROUND: In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. RESULTS: All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. CONCLUSION: The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons

Coupling local renewable energy production with electric vehicle charging: a survey of the French case

The share of renewable energy sources (RES)’ production in energy mixes, especially the ones of PV panels and wind farms, has been continuously increasing during the last few years. Similarly, a strong development of battery electric vehicles (EV) is expected within the next years. However, these two new innovations could trigger security issues on electrical grids, in particular local congestions and voltage deviations from the required standards. One way to mitigate these problems could be to combine the charging periods of the EVs with the local RES production. This paper aims at analysing the possibility to implement this kind of smart charging strategy in France by 2020, taking into account the wide diversity of local energy mixes in France and their seasonal dependencies. First, the authors identify four different energy mixes representative of most of the local French mixes, each one related to a region in France. Then, we model the charging load curves of the EVs at the substation level for the same regions. We deduce the “green charging ratio” (GCR) without any charging management strategy. The same ratio is then computed assuming that an Energy Management System (EMS), which goal is to maximize this ratio, controls the EV charging patterns. The results are provided for each region and seasons. They show a wide diversity of green charging ratio achievable: in very windy regions, the GCR without any EMS is already rather high; on the contrary, in sunny regions, the GCR is much improved with the implementation of the EMS. In such regions, the GCR can also be enhanced with the penetration of charging stations at working places

Coupling local renewable energy production with electric vehicle charging: a survey of the French case

The share of renewable energy sources (RES)’ production in energy mixes, especially the ones of PV panels and wind farms, has been continuously increasing during the last few years. Similarly, a strong development of battery electric vehicles (EV) is expected within the next years. However, these two new innovations could trigger security issues on electrical grids, in particular local congestions and voltage deviations from the required standards. One way to mitigate these problems could be to combine the charging periods of the EVs with the local RES production. This paper aims at analysing the possibility to implement this kind of smart charging strategy in France by 2020, taking into account the wide diversity of local energy mixes in France and their seasonal dependencies. First, the authors identify four different energy mixes representative of most of the local French mixes, each one related to a region in France. Then, we model the charging load curves of the EVs at the substation level for the same regions. We deduce the “green charging ratio” (GCR) without any charging management strategy. The same ratio is then computed assuming that an Energy Management System (EMS), which goal is to maximize this ratio, controls the EV charging patterns. The results are provided for each region and seasons. They show a wide diversity of green charging ratio achievable: in very windy regions, the GCR without any EMS is already rather high; on the contrary, in sunny regions, the GCR is much improved with the implementation of the EMS. In such regions, the GCR can also be enhanced with the penetration of charging stations at working places

Innovation et règles inefficaces : le cas des véhicules électriques

International audienceAbstract (En) Electric Vehicles (EVs) can be used as distributed storage units to provide Transmission System Operators (TSOs) with reserve power. This solution has been demonstrated as viable from an economic perspective. However, market design considerations are rarely taken into account in the studies dealing with this topic. We find that market rules can have a significant impact on the expected revenues of an EV fleet providing TSO reserve. In this paper, the authors are concerned with identifying the most important rules, and numbering their impacts on the possible revenues for an EV fleet.Utiliser les Véhicules Électriques (VE) pour fournir de la réserve de puissance au Gestionnaire de réseau de Transport (GRT) a été démontré comme une solution économiquement viable dans nombre d'expériences internationales. Les VE étant des petites unités de stockage, ils aident le système à s'équilibrer en temps-réel. Cependant, les études menées sur ce sujet prennent rarement en compte les règles économiques mises en place pour organiser la participation des VE aux services système. Ce faisant, nous constatons que ces règles peuvent avoir un impact important sur les revenus escomptés. Ainsi, ce papier modélise l'impact de ces règles sur la capacité des VE à fournir de la réserve de puissance au GRT et estime leur rémunération-ou leur absence-si les règles inefficaces actuelles persistent

INTERPRO

InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core. Each combined InterPro entry includes functional descriptions and literature references, and links are made back to the relevant parent database(s), allowing users to see at a glance whether a particular family or domain has associated patterns, profiles, fingerprints, etc.. Merged and individual entries (i.e., those that have no counterpart in the companion resources) are assigned unique accession numbers. The first release of InterPro contains around 2,400 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 4,300 regular expressions, profiles, fingerprints and Hidden Markov Models (HMMs). Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 370,000 hits in total). The database is accessible for text-based searches at http://www.ebi.ac.uk/ interpro/