Isoforms

Programs

Python

Python-based applications use isoform.py for common functions.

• cmpiso - compares collections of isoforms in GFF
• geniso - generates isoforms and their probabilities
• modelbuilder - creates the various model files
• optiso - optimizes model parameters with a genetic algorithm
• run_apc - builds Makefile to run isoformer and optiso on apc set

C

The genomikon repo contains a couple of faster implementations in the isoformer directory.

• isoformer - this is the same as geniso but ~100x faster
• isocounter - as above, but only counting, not calculating probabilities
• isorandom - counting isoforms in random sequences

Utilities

• conformity.py - compares outputs of geniso and isoformer
• optiso-mp - multi-processing version with some odd bugs
• speedo.py - compares speeds of geniso and isoformer
• summary.py - creates TSV of the apc set

Data

Data collection is described in datacore2024/project_splicing. The 1045 genes of the smallgenes dataset.

Models

See the models directory for standard models and modelbuilder for how to build the models.

Trivia

There are 19.938 billion RNASeq_splice records in WormBase. As a rough estimate of intron frequency, divide intron counts by 20 billion.