A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

<p>Abstract</p> <p>Background</p> <p>Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences.</p> <p>Results</p> <p>In this paper, a novel building block of proteins called Top-<it>n</it>-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-<it>n</it>-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-<it>n</it>-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-<it>n</it>-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-<it>n</it>-grams and LSA gives significantly better results compared to related methods.</p> <p>Conclusion</p> <p>The method based on Top-<it>n</it>-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-<it>n</it>-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.</p

STUDIES ON WASTE-WATER TREATMENT BY MEANS OF INTEGRATED BIOLOGICAL POND SYSTEM - DESIGN AND FUNCTION OF MACROPHYTES

A biological treatment pond system to purify municipal wastewater from a medium-sized city has been operated for 3 years and gained good results. Macrophytes took a very important part in this system. The macrophyte ponds and zones were designed spacially and periodically different to test their purification efficiencies.The purifing system was divided into three functional zones: purifing zone, effluent upgrading zone and multi-utilization zone. Macrophytes were planted in several subzones in series in some ponds. The experiments showed that the multi-macrophyte zone system revealed greater purification efficiencies than those of traditional oxidation ponds as well as general macrophyte ponds. The system reached high reductions of COD, BOD, TSS, TN and TP. The activity of mutagenic agents and numbers of virus and bacteria were significantly decreased during the process of purification. The effluent from the system was greatly upgraded and could be used in fishery and agriculture. The harvested macrophytes from the purifing zone and effluent upgrading zone could be put into the multi-utilization zone as feed, fertilizer, biogas, etc. The idea of resourcization of wastewater was being put into practice. The studies also showed that some macrophytes revealed strong ability to inhibit algae growth not because of light, nutrient and space competition. These results had been used in the treatment system design and gained expected effects. Plant harvesting did not yield dramatic effects on reductions of the main pollutants, though it did affect remarkably the biomass productivity of the macrophytes

STUDIES ON WASTE-WATER TREATMENT BY MEANS OF INTEGRATED BIOLOGICAL POND SYSTEM - DESIGN AND FUNCTION OF MACROPHYTES

A biological treatment pond system to purify municipal wastewater from a medium-sized city has been operated for 3 years and gained good results. Macrophytes took a very important part in this system. The macrophyte ponds and zones were designed spacially and periodically different to test their purification efficiencies.The purifing system was divided into three functional zones: purifing zone, effluent upgrading zone and multi-utilization zone. Macrophytes were planted in several subzones in series in some ponds. The experiments showed that the multi-macrophyte zone system revealed greater purification efficiencies than those of traditional oxidation ponds as well as general macrophyte ponds. The system reached high reductions of COD, BOD, TSS, TN and TP. The activity of mutagenic agents and numbers of virus and bacteria were significantly decreased during the process of purification. The effluent from the system was greatly upgraded and could be used in fishery and agriculture. The harvested macrophytes from the purifing zone and effluent upgrading zone could be put into the multi-utilization zone as feed, fertilizer, biogas, etc. The idea of resourcization of wastewater was being put into practice. The studies also showed that some macrophytes revealed strong ability to inhibit algae growth not because of light, nutrient and space competition. These results had been used in the treatment system design and gained expected effects. Plant harvesting did not yield dramatic effects on reductions of the main pollutants, though it did affect remarkably the biomass productivity of the macrophytes