MethylSeqLogo: DNA methylation smart sequence logos.

ABSTRACT:

Background

Some transcription factors, MYC for example, bind sites of potentially methylated DNA. This may increase binding specificity as such sites are (1) highly under-represented in the genome, and (2) offer additional, tissue specific information in the form of hypo- or hyper-methylation. Fortunately, bisulfite sequencing data can be used to investigate this phenomenon.

Method

We developed MethylSeqLogo, an extension of sequence logos which includes new elements to indicate DNA methylation and under-represented dimers in each position of a set binding sites. Our method displays information from both DNA strands, and takes into account the sequence context (CpG or other) and genome region (promoter versus whole genome) appropriate to properly assess the expected backgrou

SUBMITTER: Hsu FM 

PROVIDER: S-EPMC11462690 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature