imeter

2022 reboot of IME project. Starting over from the beginning with Python.

Data

The at_ime_master.gz file contains information about most introns in the A.thaliana genome (copied from KorfLab/datacore/project_imeter).

The file is tab-separated and has the following columns

• Transcript ID
• Intron begin relative to start of gene
• Intron end relative to start of gene
• Strand of the gene in the genome
• 11 expression values (RNA-seq splice junctions) for various tissues
  • Aerial
  • Carpel
  • Dark Grown Seedling
  • Light Grown Seedling
  • Leaf
  • Pollen
  • Receptacle
  • Root Apical Meristem
  • Root
  • Shoot Apical Meristem
  • Stage 12 Flower
• Sequence of the intron

The file looks like this (4 lines shown of 142,779):

AT3G02220.1     1057    1151    -       380     349     601     2717    3010    3       489     321     1010    49      499     GTAAGCTTCTCTAGTTACTTTGAAGAGTTTTTGAGATTTGTAAATGTGTATGTTTGTGTGATTTGGTCCTGAAGTTGCGTATTTGCTTGACATAG
AT3G02220.1     914     1008    -       362     302     677     2889    3291    0       462     373     1170    9       655     GTTTGTCTTTTAATTATTCCGCTTTTGGCTTCTAATGTTCAATTTCATGCTTGTTTTTGGGAGGTTGTTGCTGATTTCTTATTGATGTGATGCAG
AT3G02220.1     753     870     -       331     309     542     2861    2968    2       504     340     839     48      503     GTACTTGTACCTTGAAGACAGTCTTTCTTCTACTTATGCTAGATGCTGGTTTCCTTAAGAGTGGGTTTAGTAGACAAGATATTAAACTAATCTTGAGGTAATTATTCGTTTCTCGCAG
AT3G02220.1     565     688     -       283     249     571     2568    2308    5       471     374     697     25      265     GTTAGTGTTTTCTTTCTTTGCTTTTGTTCTCGTACTTTCTTGGCTAATTAGAGTGTATAGATCAGTATCTTGTTTTATAAGTTGATGTGTTATGGTATTGAAATGGGTATGAAACTGATAACAG

Version 1

The v1 directory contains a reimplementation of IMEter version 1.0 as published. The results will be a little different because the training set for the original version is different from the at_ime_master.gz included in the data directory.

Version 3

The v3 directory contains some ideas of a better implementation of IMEter 1.0. It is not a follow-up of version 2.0. Some things to address in version 3:

• Counting of both strands.
• Not splitting the data set into proximal and distal. Instead, use a proximal weight based on distance. Distal weight is 1 - proximal.

Notes

• Leaf tissue is where the original experiments were done
• Something with tissues in the next experiments?
• Deal with alternative isoforms somehow

EIE things

In an effort to find orthologous and paralogous introns across species, there is an eie.fa file that has exon-intron-exon sequences. The introns are chosen to be good IME candidates. See the eie_build.py script for how this works.