apa: alternative polyadenylation (APA) analysis
apa is a Python framework for processing and analysing 3'-end targeted sequence data to study alternative polyadenylation. apa interconnects pybio (basic handling of annotated genomes), RNAmotifs2 (analysis of regulatory motif clusters) and other open-source software (DEXSeq, STAR short-read aligner).
The inclusive nature of the framework, together with novel integrative solutions (differential polyA site usage and RNA-protein binding via RNA-maps, cluster motif analysis), results in the following computational capabilities:
- management of diverse high-throughput sequencing datasets (pre-processing, alignment, annotation),
- polyA site database (atlas) construction and comparison to existing polyA resources,
- identification of genes that undergo alternative polyadenylation (DEXSeq),
- identification of motifs influencing polyA site choice (RNAmotifs2),
- identification of motifs influencing alternative splicing (DEXSeq and RNAmotifs2),
- integration with iCLIP (RNA-protein binding) and computing RNA-maps,
- and other.
The development started in 2009 when Tomaž Curk and Gregor Rot wrote the first prototype of apa. In 2013, Gregor Rot refactored and further developed the code, also establishing expressRNA, a web application for exploring results of alternative polyadenylation analysis.
High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43
Rot, G., Wang, Z., Huppertz, I., Modic, M., Lenče, T., Hallegger, M., Haberman, N., Curk, T., von Mering, C., Ule, J.
Cell Reports , Volume 19 , Issue 5 , 1056 - 1067
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