DNAdesign: feature-aware in silico design of synthetic DNA through mutation.

ABSTRACT:

Motivation

DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.

Results

DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all

SUBMITTER: Wang Y 

PROVIDER: S-EPMC11825384 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature