iRSpot-ADPM: Identify recombination spots by incorporating the associated dinucleotide product model into Chou's pseudo components

DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features

In the domain of genome annotation, the identification of DNA-binding protein is one of the crucial challenges. DNA is considered a blueprint for the cell. It contained all necessary information for building and maintaining the trait of an organism. It is DNA, which makes a living thing, a living thing. Protein interaction with DNA performs an essential role in regulating DNA functions such as DNA repair, transcription, and regulation. Identification of these proteins is a crucial task for understanding the regulation of genes. Several methods have been developed to identify the binding sites of DNA and protein depending upon the structures and sequences, but they were costly and time-consuming. Therefore, we propose a methodology named “DNAPred_Prot”, which uses various position and frequency-dependent features from protein sequences for efficient and effective prediction of DNA-binding proteins. Using testing techniques like 10-fold cross-validation and jackknife testing an accuracy of 94.95% and 95.11% was yielded, respectively. The results of SVM and ANN were also compared with those of a random forest classifier. The robustness of the proposed model was evaluated by using the independent dataset PDB186, and an accuracy of 91.47% was achieved by it. From these results, it can be predicted that the suggested methodology performs better than other extant methods for the identification of DNA-binding proteins.

iTAGPred: A Two-Level Prediction Model for Identification of Angiogenesis and Tumor Angiogenesis Biomarkers

A crucial biological process called angiogenesis plays a vital role in migration, growth, and wound healing of endothelial cells and other processes that are controlled by chemical signals. Angiogenesis is the process that controls the growth of blood vessels within tissues while angiogenesis proteins play a significant role in the proper working of this process. The balancing of these signals is necessary for the proper working of angiogenesis. Unbalancing of these signals increases blood vessel formation, which causes abnormal growth or several diseases including cancer. The proposed work focuses on developing a two-layered prediction model using different classifiers like random forest (RF), neural network, and support vector machine. The first level performs in silico identification of angiogenesis proteins based on the primary structure. In the case the protein is an angiogenesis protein, then the second level predicts whether the protein is linked with tumor angiogenesis or not. The performance of the model is evaluated through various validation techniques. The model was evaluated using k-fold cross-validation, independent, self-consistency, and jackknife testing. The overall accuracy using an RF classifier for angiogenesis at the first level was 97.8% and for tumor angiogenesis at the second level was 99.5%, ANN showed 94.1% accuracy for angiogenesis and 79.9% for tumor angiogenesis, and the accuracy of SVM for angiogenesis was 78.8% and for tumor angiogenesis was 65.19%.

iRspot-DCC: Recombination hot/ cold spots identification based on dinucleotide-based correlation coefficient and convolutional neural network

The correct identification of gene recombination cold/hot spots is of great significance for studying meiotic recombination and genetic evolution. However, most of the existing recombination spots recognition methods ignore the global sequence information hidden in the DNA sequence, resulting in their low recognition accuracy. A computational predictor called iRSpot-DCC was proposed in this paper to improve the accuracy of cold/hot spots identification. In this approach, we propose a feature extraction method based on dinucleotide correlation coefficients that focus more on extracting potential DNA global sequence information. Then, 234 representative features vectors are filtered by SVM weight calculation. Finally, a convolutional neural network with better performance than SVM is selected as a classifier. The experimental results of 5-fold cross-validation test on two standard benchmark datasets showed that the prediction accuracy of our recognition method reached 95.11%, and the Mathew correlation coefficient (MCC) reaches 90.04%, outperforming most other methods. Therefore, iRspot-DCC is a high-precision cold/hot spots identification method for gene recombination, which effectively extracts potential global sequence information from DNA sequences.

iORI-ENST: identifying origin of replication sites based on elastic net and stacking learning

DNA replication is not only the basis of biological inheritance but also the most fundamental process in all living organisms. It plays a crucial role in the cell-division cycle and gene expression regulation. Hence, the accurate identification of the origin of replication sites (ORIs) has a great meaning for further understanding the regulatory mechanism of gene expression and treating genic diseases. In this paper, a novel, feasible and powerful model, namely, iORI-ENST is designed for identifying ORIs. Firstly, we extract the different features by incorporating mono-nucleotide binary encoding and dinucleotide-based spatial autocorrelation. Subsequently, elastic net is utilized as the feature selection method to select the optimal feature set. And then stacking learning is employed to predict ORIs and non-ORIs, which contains random forest, adaboost, gradient boosting decision tree, extra trees and support vector machine. Finally, the ORI sites are identified on the benchmark datasets S1 and S2 with their accuracies of 91.41% and 95.07%, respectively. Meanwhile, an independent dataset S3 is employed to verify the validation and transferability of our model and its accuracy reaches 91.10%. Comparing with state-of-the-art methods, our model achieves more remarkable performance. The results show our model is a feasible, effective and powerful tool for identifying ORIs. The source code and datasets are available at https://github.com/YingyingYao/iORI-ENST.

iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition

Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious. To address this problem, here, we propose a novel computational model namely iPhosH-PseAAC for prediction of phosphohistidine sites in a given protein sequence using pseudo amino acid composition (PseAAC), statistical moments, and position relative features. The results of the proposed predictor are validated through self-consistency testing, 10-fold cross-validation, and jackknife testing. The self-consistency validation gave the 100 percent accuracy, whereas, for cross-validation, the accuracy achieved is 94.26 percent. Moreover, jackknife testing gave 97.07 percent accuracy for the proposed model. Thus, the proposed model iPhosH-PseAAC for prediction of iPhosH site has the great ability to predict the PhosH sites in given proteins.

Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks

Prediction of protein subcellular location has currently become a hot topic because it has been proven to be useful for understanding both the disease mechanisms and novel drug design. With the rapid development of automated microscopic imaging technology in recent years, classification methods of bioimage-based protein subcellular location have attracted considerable attention for images can describe the protein distribution intuitively and in detail. In the current study, a prediction method of protein subcellular location was proposed based on multi-view image features that are extracted from three different views, including the four texture features of the original image, the global and local features of the protein extracted from the protein channel images after color segmentation, and the global features of DNA extracted from the DNA channel image. Finally, the extracted features were combined together to improve the performance of subcellular localization prediction. From the performance comparison of different combination features under the same classifier, the best ensemble features could be obtained. In this work, a classifier based on Stacked Auto-encoders and the random forest was also put forward. To improve the prediction results, the deep network was combined with the traditional statistical classification methods. Stringent cross-validation and independent validation tests on the benchmark dataset demonstrated the efficacy of the proposed method.

Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach

Meiotic recombination is the driving force of evolutionary development and an important source of genetic variation. The meiotic recombination does not take place randomly in a chromosome but occurs in some regions of the chromosome. A region in chromosomes with higher rate of meiotic recombination events are considered as hotspots and a region where frequencies of the recombination events are lower are called coldspots. Prediction of meiotic recombination spots provides useful information about the basic functionality of inheritance and genome diversity. This study proposes an intelligent computational predictor called iRSpots-DNN for the identification of recombination spots. The proposed predictor is based on a novel feature extraction method and an optimized deep neural network (DNN). The DNN was employed as a classification engine whereas, the novel features extraction method was developed to extract meaningful features for the identification of hotspots and coldspots across the yeast genome. Unlike previous algorithms, the proposed feature extraction avoids bias among different selected features and preserved the sequence discriminant properties along with the sequence-structure information simultaneously. This study also considered other effective classifiers named support vector machine (SVM), K-nearest neighbor (KNN), and random forest (RF) to predict recombination spots. Experimental results on a benchmark dataset with 10-fold cross-validation showed that iRSpots-DNN achieved the highest accuracy, i.e., 95.81%. Additionally, the performance of the proposed iRSpots-DNN is significantly better than the existing predictors on a benchmark dataset. The relevant benchmark dataset and source code are freely available at: https://github.com/Fatima-Khan12/iRspot_DNN/tree/master/iRspot_DNN.

A Novel Amino Acid Properties Selection Method for Protein Fold Classification

BACKGROUND

Amino acid physicochemical properties encoded in protein primary structure play a crucial role in protein folding. However, it is not yet clear which of the properties are the most suitable for protein fold classification.

OBJECTIVE

To avoid exhaustively searching the total properties space, an amino acid properties selection method was proposed in this study to rapidly obtain a suitable properties combination for protein fold classification.

METHODS

The proposed amino acid properties selection method was based on sequential floating forward selection strategy. Beginning with an empty set, variable number of features were added iteratively until achieving the iteration termination condition.

RESULTS

The experimental results indicate that the proposed method improved prediction accuracies by 0.26-5% on a widely used benchmark dataset with appropriately selected amino acid properties.

CONCLUSION

The proposed properties selection method can be extended to other biomolecule property related classification problems in bioinformatics.

Some illuminating remarks on molecular genetics and genomics as well as drug development

Facing the explosive growth of biological sequences unearthed in the post-genomic age, one of the most important but also most difficult problems in computational biology is how to express a biological sequence with a discrete model or a vector, but still keep it with considerable sequence-order information or its special pattern. To deal with such a challenging problem, the ideas of "pseudo amino acid components" and "pseudo K-tuple nucleotide composition" have been proposed. The ideas and their approaches have further stimulated the birth for "distorted key theory", "wenxing diagram", and substantially strengthening the power in treating the multi-label systems, as well as the establishment of the famous "5-steps rule". All these logic developments are quite natural that are very useful not only for theoretical scientists but also for experimental scientists in conducting genetics/genomics analysis and drug development. Presented in this review paper are also their future perspectives; i.e., their impacts will become even more significant and propounding.

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae

Meiotic recombination is one of the most important driving forces of biological evolution, which is initiated by double-strand DNA breaks. Recombination has important roles in genome diversity and evolution. This review firstly provides a comprehensive survey of the 15 computational methods developed for identifying recombination hotspots in Saccharomyces cerevisiae. These computational methods were discussed and compared in terms of underlying algorithms, extracted features, predictive capability and practical utility. Subsequently, a more objective benchmark data set was constructed to develop a new predictor iRSpot-Pse6NC2.0 (http://lin-group.cn/server/iRSpot-Pse6NC2.0). To further demonstrate the generalization ability of these methods, we compared iRSpot-Pse6NC2.0 with existing methods on the chromosome XVI of S. cerevisiae. The results of the independent data set test demonstrated that the new predictor is superior to existing tools in the identification of recombination hotspots. The iRSpot-Pse6NC2.0 will become an important tool for identifying recombination hotspot.

i6mA-DNCP: Computational Identification of DNA N6-Methyladenine Sites in the Rice Genome Using Optimized Dinucleotide-Based Features

DNA N⁶-methyladenine (6mA) plays an important role in regulating the gene expression of eukaryotes. Accurate identification of 6mA sites may assist in understanding genomic 6mA distributions and biological functions. Various experimental methods have been applied to detect 6mA sites in a genome-wide scope, but they are too time-consuming and expensive. Developing computational methods to rapidly identify 6mA sites is needed. In this paper, a new machine learning-based method, i6mA-DNCP, was proposed for identifying 6mA sites in the rice genome. Dinucleotide composition and dinucleotide-based DNA properties were first employed to represent DNA sequences. After a specially designed DNA property selection process, a bagging classifier was used to build the prediction model. The jackknife test on a benchmark dataset demonstrated that i6mA-DNCP could obtain 84.43% sensitivity, 88.86% specificity, 86.65% accuracy, a 0.734 Matthew's correlation coefficient (MCC), and a 0.926 area under the receiver operating characteristic curve (AUC). Moreover, three independent datasets were established to assess the generalization ability of our method. Extensive experiments validated the effectiveness of i6mA-DNCP.

pLoc_bal-mVirus: Predict Subcellular Localization of Multi-Label Virus Proteins by Chou's General PseAAC and IHTS Treatment to Balance Training Dataset

Background/Objective:

Knowledge of protein subcellular localization is vitally important for both basic research and drug development. Facing the avalanche of protein sequences emerging in the post-genomic age, it is urgent to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information alone. Recently, a predictor called “pLoc-mVirus” was developed for identifying the subcellular localization of virus proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, known as “multiplex proteins”, may simultaneously occur in, or move between two or more subcellular location sites. Despite the fact that it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mVirus was trained by an extremely skewed dataset in which some subset was over 10 times the size of the other subsets. Accordingly, it cannot avoid the biased consequence caused by such an uneven training dataset.

Methods:

Using the Chou's general PseAAC (Pseudo Amino Acid Composition) approach and the IHTS (Inserting Hypothetical Training Samples) treatment to balance out the training dataset, we have developed a new predictor called “pLoc_bal-mVirus” for predicting the subcellular localization of multi-label virus proteins.

Results:

Cross-validation tests on exactly the same experiment-confirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mVirus, the existing state-of-theart predictor for the same purpose.

Conclusion:

Its user-friendly web-server is available at http://www.jci-bioinfo.cn/pLoc_balmVirus/, by which the majority of experimental scientists can easily get their desired results without the need to go through the detailed complicated mathematics. Accordingly, pLoc_bal-mVirus will become a very useful tool for designing multi-target drugs and in-depth understanding of the biological process in a cell.

iDHS-DMCAC: identifying DNase I hypersensitive sites with balanced dinucleotide-based detrending moving-average cross-correlation coefficient

DNase I hypersensitive sites (DHSs) are associated with regulatory DNA elements, so their good understanding is significant for both the biomedical research and the discovery of new drugs. Traditional experimental methods are laborious, time consuming and an inaccurately task to detect DHSs. More importantly, with the avalanche of genome sequences in the postgenomic age, it is highly essential to develop cost-effective computational approaches to identify DHSs. In this paper, we develop a statistical feature extraction model using the detrended moving-average cross-correlation (DMCA) coefficient descriptor based on dinucleotide property matrix generated by the 15 DNA dinucleotide properties, and this model is named iDHS-DMCAC. A 105-dimensional feature vector is constructed for a certain window on the two class imbalanced benchmark datasets, with over-sampling and support vector machine algorithms. Rigorous cross-validations indicate that our predictor remarkably outperforms the existing models in both accuracy and stability. We anticipate that iDHS-DMCAC will become a very useful high throughput tool, or at the very least, a complementary tool to the existing methods of identifying DNase I hypersensitive sites. The datasets and source codes of the proposed model are freely available at https://github.com/shengli0201/Datasets .

An ensemble method for multi-type Gram-negative bacterial secreted protein prediction by integrating different PSSM-based features

In Gram-negative bacteria, a wide range of proteins are secreted by highly specialized secretion systems. These secreted proteins play essential roles in the response of bacteria to their environment and also in several physiological processes such as adhesion, pathogenicity, adaptation and survival. Therefore, identifying secreted proteins in Gram-negative bacteria may assist in understanding the secretion mechanism and development of new antimicrobial strategies. Considering that a single-feature model is less likely to comprehensively cover this information, three kinds of feature models were used in this paper to represent protein samples by composition analysis, correlation analysis and smoothing encoding method on position-specific scoring matrix profiles. A support vector machine-based ensemble method with these hybrid features was developed to predict multi-type Gram-negative bacterial secreted proteins. Finally, our method achieves overall accuracies of 97.09% and 96.51% using an independent dataset test and jackknife test on a public test dataset, which are 3.49% and 2.32% higher, respectively, than results obtained by other methods. These results show the effectiveness and stability of the proposed ensemble method. It is anticipated that our method will provide useful information for further research on bacterial secreted proteins and secreted systems.

iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition

The promoter is a regulatory DNA region about 81-1000 base pairs long, usually located near the transcription start site (TSS) along upstream of a given gene. By combining a certain protein called transcription factor, the promoter provides the starting point for regulated gene transcription, and hence plays a vitally important role in gene transcriptional regulation. With explosive growth of DNA sequences in the post-genomic age, it has become an urgent challenge to develop computational method for effectively identifying promoters because the information thus obtained is very useful for both basic research and drug development. Although some prediction methods were developed in this regard, most of them were limited at merely identifying whether a query DNA sequence being of a promoter or not. However, based on their strength-distinct levels for transcriptional activation and expression, promoter should be divided into two categories: strong and weak types. Here a new two-layer predictor, called "iPSW(2L)-PseKNC", was developed by fusing the physicochemical properties of nucleotides and their nucleotide density into PseKNC (pseudo K-tuple nucleotide composition). Its 1st-layer serves to predict whether a query DNA sequence sample is of promoter or not, while its 2nd-layer is able to predict the strength of promoters. It has been observed through rigorous cross-validations that the 1st-layer sub-predictor is remarkably superior to the existing state-of-the-art predictors in identifying the promoters and non-promoters, and that the 2nd-layer sub-predictor can do what is beyond the reach of the existing predictors. Moreover, the web-server for iPSW(2L)-PseKNC has been established at http://www.jci-bioinfo.cn/iPSW(2L)-PseKNC, by which the majority of experimental scientists can easily get the results they need.

Relationship Between DNA Methylation in Key Region and the Differential Expressions of Genes in Human Breast Tumor Tissue

Breast cancer has a high mortality rate for females. Aberrant DNA methylation plays a crucial role in the occurrence and progression of breast carcinoma. By comparing DNA methylation differences between tumor breast tissue and normal breast tissue, we calculate and analyze the distributions of the hyper- and hypomethylation sites in different function regions. Results indicate that enhancer regions are often hypomethylated in breast cancer. CpG islands (CGIs) are mainly hypermethylated, while the flanking CGI (shores and shelves) is more easily hypomethylated. The hypomethylation in gene body region is related to the upregulation of gene expression, and the hypomethylation of enhancer regions is closely associated with gene expression upregulation in breast cancer. Some key hypomethylation sites in enhancer regions and key hypermethylation sites in CGIs for regulating key genes are, respectively, found, such as oncogenes ESR1 and ERBB2 and tumor suppressor genes FBLN2, CEBPA, and FAT4. This suggests that the recognizing methylation status of these genes will be useful for the diagnosis of breast cancer.

Predicting membrane proteins and their types by extracting various sequence features into Chou's general PseAAC

For many biological functions membrane proteins (MPs) are considered crucial. Due to this nature of MPs, many pharmaceutical agents have reflected them as attractive targets. It bears indispensable importance that MPs are predicted with accurate measures using effective and efficient computational models (CMs). Annotation of MPs using in vitro analytical techniques is time-consuming and expensive; and in some cases, it can prove to be intractable. Due to this scenario, automated prediction and annotation of MPs through CM based techniques have appeared to be useful. Based on the use of computational intelligence and statistical moments based feature set, an MP prediction framework is proposed. Furthermore, the previously used dataset has been enhanced by incorporating new MPs from the latest release of UniProtKB. Rigorous experimentation proves that the use of statistical moments with a multilayer neural network, trained using back-propagation based prediction techniques allows more thorough results.

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition

As a prevalent post-transcriptional modification, N⁶-methyladenosine (m⁶A) plays key roles in a series of biological processes. Although experimental technologies have been developed and applied to identify m⁶A sites, they are still cost-ineffective for transcriptome-wide detections of m⁶A. As good complements to the experimental techniques, some computational methods have been proposed to identify m⁶A sites. However, their performance remains unsatisfactory. In this study, we firstly proposed an Euclidean distance based method to construct a high quality benchmark dataset. By encoding the RNA sequences using pseudo nucleotide composition, a new predictor called iRNA(m6A)-PseDNC was developed to identify m⁶A sites in the Saccharomyces cerevisiae genome. It has been demonstrated by the 10-fold cross validation test that the performance of iRNA(m6A)-PseDNC is superior to the existing methods. Meanwhile, for the convenience of most experimental scientists, established at the site http://lin-group.cn/server/iRNA(m6A)-PseDNC.php is its web-server, by which users can easily get their desired results without need to go through the detailed mathematics. It is anticipated that iRNA(m6A)-PseDNC will become a useful high throughput tool for identifying m⁶A sites in the S. cerevisiae genome.

Implications of Newly Identified Brain eQTL Genes and Their Interactors in Schizophrenia

Schizophrenia (SCZ) is a devastating genetic mental disorder. Identification of the SCZ risk genes in brains is helpful to understand this disease. Thus, we first used the minimum Redundancy-Maximum Relevance (mRMR) approach to integrate the genome-wide sequence analysis results on SCZ and the expression quantitative trait locus (eQTL) data from ten brain tissues to identify the genes related to SCZ. Second, we adopted the variance inflation factor regression algorithm to identify their interacting genes in brains. Third, using multiple analysis methods, we explored and validated their roles. By means of the aforementioned procedures, we have found that (1) the cerebellum may play a crucial role in the pathogenesis of SCZ and (2) ITIH4 may be utilized as a clinical biomarker for the diagnosis of SCZ. These interesting findings may stimulate novel strategy for developing new drugs against SCZ. It has not escaped our notice that the approach reported here is of use for studying many other genome diseases as well.

iMethyl-STTNC: Identification of N6-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences

N⁶- methyladenosine (m⁶A) is a vital post-transcriptional modification, which adds another layer of epigenetic regulation at RNA level. It chemically modifies mRNA that effects protein expression. RNA sequence contains many genetic code motifs (GAC). Among these codes, identification of methylated or not methylated GAC motif is highly indispensable. However, with a large number of RNA sequences generated in post-genomic era, it becomes a challenging task how to accurately and speedily characterize these sequences. In view of this, the concept of an intelligent is incorporated with a computational model that truly and fast reflects the motif of the desired classes. An intelligent computational model "iMethyl-STTNC" model is proposed for identification of methyladenosine sites in RNA. In the proposed study, four feature extraction techniques, such as; Pseudo-dinucleotide-composition, Pseudo-trinucleotide-composition, split-trinucleotide-composition, and split-tetra-nucleotides-composition (STTNC) are utilized for genuine numerical descriptors. Three different classification algorithms including probabilistic neural network, Support vector machine (SVM), and K-nearest neighbor are adopted for prediction. After examining the outcomes of prediction model on each feature spaces, SVM using STTNC feature space reported the highest accuracy of 69.84%, 91.84% on dataset1 and dataset2, respectively. The reported results show that our proposed predictor has achieved encouraging results compared to the present approaches, so far in the research. It is finally reckoned that our developed model might be beneficial for in-depth analysis of genomes and drug development.

iRSpot-SF: Prediction of recombination hotspots by incorporating sequence based features into Chou's Pseudo components

Recombination hotspots in a genome are unevenly distributed. Hotspots are regions in a genome that show higher rates of meiotic recombinations. Computational methods for recombination hotspot prediction often use sophisticated features that are derived from physico-chemical or structure based properties of nucleotides. In this paper, we propose iRSpot-SF that uses sequence based features which are computationally cheap to generate. Four feature groups are used in our method: k-mer composition, gapped k-mer composition, TF-IDF of k-mers and reverse complement k-mer composition. We have used recursive feature elimination to select 17 top features for hotspot prediction. Our analysis shows the superiority of gapped k-mer composition and reverse complement k-mer composition features over others. We have used SVM with RBF kernel as a classification algorithm. We have tested our algorithm on standard benchmark datasets. Compared to other methods iRSpot-SF is able to produce significantly better results in terms of accuracy, Mathew's Correlation Coefficient and sensitivity which are 84.58%, 0.6941 and 84.57%. We have made our method readily available to use as a python based tool and made the datasets and source codes available at: https://github.com/abdlmaruf/iRSpot-SF. An web application is developed based on iRSpot-SF and freely available to use at: http://irspot.pythonanywhere.com/server.html.