Pavlovic, M. — Page 2 | Search bioRxiv

bioRxiv2019

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking

SummaryB- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full length variable region immune receptor sequences. ImmuneSIM enables the tuning of the immune receptor features: (i) species and chain type (BCR, TCR, single, paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation, and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis, and machine learning methods for motif detection.\n\nAvailabilityThe package is available via https://github.com/GreiffLab/immuneSIM and will also be available at CRAN (submitted). The documentation is hosted at https://immuneSIM.readthedocs.io.\n\nContactvictor.greiff@medisin.uio.no, sai.reddy@ethz.ch

bioinformatics↗

bioRxiv2018

Target Binding and Sequence Prediction With LSTMs

Deep recurrent neural networks (DRNNs) have recently demonstrated strong performance in sequential data analysis, such as natural language processing. These capabilities make them a promising tool for inferential analysis of sequentially structured bioinformatics data as well. Here, we assessed the ability of Long Short-Term Memory (LSTM) networks, a class of DRNNs, to predict properties of proteins based on their primary structures. The proposed architecture is trained and tested on two different datasets to predict whether a given sequence falls into a certain class or not. The first dataset, directly imported from Uniprot, was used to train the network on whether a given protein contained or did not contain a conserved sequence (homeodomain), and the second dataset, derived by literature mining, was used to train a network on whether a given protein binds or doesnt bind to Artemisinin, a drug typically used to treat malaria. In each case, the model was able to differentiate between the two different classes of sequences it was given with high accuracy, illustrating successful learning and generalization. Upon completion of training, an ROC curve was created using the homeodomain and artemisinin validation datasets. The AUC of these datasets was 0.80 and 0.87 respectively, further indicating the models effectiveness. Furthermore, using these trained models, it was possible to derive a protocol for sequence detection of homeodomain and binding motif, which are well-documented in literature, and a known Artemisinin binding site, respectively [1-3]. Along with these contributions, we developed a python API to directly connect to Uniprot data sourcing, train deep neural networks on this primary sequence data using TensorFlow, and uniquely visualize the results of this analysis. Such an approach has the potential to drastically increase accuracy and reduce computational time and, current major limitations in informatics, from inquiry to discovery in protein function research.

bioinformatics↗