pwmU12db: PWM of U12 and U2-type introns splice sites

In IntEREst: Intron-Exon Retention Estimator

Description

PWM of U12 and U2-type introns splice sites and it is based on the U12DB database.

Usage

data("pwmU12db")

Format

A list that contains Position Weight Matrices (PWM) of donor site, branch point and acceptor site of U12-type introns and the PWMs of donor site and acceptor site of U2-type introns. It is based on the U12DB database.

pwmDonU12

A position weigh matrix for the donor site of the U12-type introns, with 4 rows and 46 columns. The rows of the matrix represent "A", "C", "G", and "T" nucleotides and the columns represent the postions in the genome. Each position in the matrix include a weight (i.e. number between 0 and 1) which indicates how common the corresponding base (represented by the row of the matrix) is observed in the corerespoding position (represented by the colum of the matrix).

pwmBpU12

A position weigh matrix for the branch point of the U12-type introns, with 4 rows and 9 columns.

pwmAccU12

A position weigh matrix for the acceptor site of the U12-type introns, with 4 rows and 46 columns.

pwmDonU2

A position weigh matrix for the donor site of the U2-type introns, with 4 rows and 25 columns.

pwmAccU2

A position weigh matrix for the acceptor site of the U12-type introns, with 4 rows and 46 columns.

Value

List of 5 numeric matrices representing the PWMs of donor site of U12-type introns, branch point site of U12-type introns, acceptor site of U12-type introns, donor site of U2-type introns, and acceptor site of U2-type introns.

Source

Alioto, T.S. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Research 2006, doi: 10.1093/nar/gkl796

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.