ORcombiner

ORcombiner is a software tool designed for biological sequence analysis, specifically for the creation of combined sequences from a set of input sequences. It is particularly useful in contexts where researchers need to merge multiple DNA or protein sequences into a single, representative sequence. This can be for various purposes, such as generating consensus sequences, designing synthetic genes, or preparing sequences for experimental validation.

The primary function of ORcombiner is to take multiple related sequences and produce a new sequence that incorporates elements from all of them. This process often involves aligning the input sequences first to identify regions of similarity and difference. Based on the alignment, the tool then constructs the output sequence, which can be a consensus sequence where the most frequent nucleotide or amino acid at each position is chosen, or it can incorporate specific variations or modifications as defined by the user.

ORcombiner typically offers options for handling ambiguities, such as introducing IUPAC codes or specific characters when there is no clear consensus. Users can often specify rules for merging, such as prioritizing certain sequences or regions. The tool is command-line based, making it suitable for integration into automated analysis pipelines and for processing large datasets efficiently. Its straightforward functionality makes it a valuable utility for molecular biologists, bioinformaticians, and genetic engineers.