Applications and use cases of RNNs in genomics

Even though FNNs and CNNs are extremely popular for tackling problems in genomics, they both have limitations. Genomics is all about sequence data, so RNNs can play a key role in several genomics applications. In addition, RNNs can find long-range dependencies in the data, which is why RNNs are great for genomic applications. RNNs are currently being used in several genomics applications, such as constructing a genotype imputation and phenotype sequences prediction system, base-calling accuracy for nanopore sequencing data, genetic regulatory networks, predicting protein functions, and so on. We’ll quickly look at a few RNN-based applications in genomics in the following section.

DeepNano

DeepNano is a freely available base caller for the Oxford Nanopore Technology (ONT) sequencing platform (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178751). Base calling is particularly important for sequencing platforms...