Modstrings

Modstrings implements internal character translation to enable working with RNA and DNA sequences containing modified nucleotides within the Biostrings package infrastructure in R.

Key Features:

• Modified nucleotide sequence classes: ModRNAString and ModDNAString classes and derivatives are implemented to represent sequences with modified nucleotides.
• Object construction and modification: Functions to construct and modify ModRNAString and ModDNAString objects despite encoding issues are implemented.
• Sequence-location conversion: Conversion from sequences to list-like location information and the reverse operation is implemented.

Scientific Applications:

• Modified nucleotide sequence representation: Enables standardized handling of RNA and DNA sequences containing modified nucleotides that use special characters from multiple sources.
• Integration with Biostrings infrastructure: Facilitates analysis of modified nucleotide sequences within the existing Bioconductor Biostrings framework in R.

Methodology:

Modified nucleotide characters are translated internally to work with the Biostrings package infrastructure.