Abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.

ABSTRACT:

Background

Transcription factor (TF) binding motifs are identified by high throughput sequencing technologies as means to capture Protein-DNA interactions. These motifs are often represented by consensus sequences in form of position weight matrices (PWMs). With ever-increasing pool of TF binding motifs from multiple sources, redundancy issues are difficult to avoid, especially when every source maintains its own database for collection. One solution can be to cluster biologically relevant or similar PWMs, whether coming from experimental detection or in silico predictions. However, there is a lack of efficient tools to cluster PWMs. Assessing quality of PWM clusters is yet another challenge. Therefore, new methods and tools are required to efficiently cluster PWMs and assess quali

SUBMITTER: Ali O 

PROVIDER: S-EPMC8896320 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature