BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.

ABSTRACT:

Motivation

Accurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.

Results

We developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five dif

SUBMITTER: Khan A 

PROVIDER: S-EPMC8275979 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature