calculateMaxEntScanScore: Calculate MaxEntScan score of a splice site sequence

In caggtaagtat/ModCon: Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Description

This function calculates the MaxEntScan score of either splice donor (SD) or acceptor sequences (SA).

Usage

calculateMaxEntScanScore(seqVector, ssType)

Arguments

seqVector	Character value of nucleotide sequence of a splice site sequence. SA sequences should be 23nt long (20 intronic, 3 exonic) and SD sequences should be 9nt long (3 exonic, 6 intronic). Only bases 'A', 'G', 'C', 'T' permitted.
ssType	Numeric value which indicates the type of splice site. Either '3' for an SA or '5' for an SD.

Value

Numeric vector stating the MaxEntScan score per splice site sequence entered with seqVector

Examples

calculateMaxEntScanScore('TTCCAAACGAACTTTTGTAGGGA',3)
calculateMaxEntScanScore('GAGGTAAGT',5)

caggtaagtat/ModCon documentation built on March 12, 2021, 4:12 a.m.