RNA Baser

Easy to use aligner software for RNA sequence contig assembly, contig editing, and mutation detection for Windows. It is a molecular biology software that can view and assemble sequences in contigs.Features: end clip, export sequences, assemblies, code detection.

RNA Baser is an affordable alternative for assembly of RNA sequences and generation of contigs. File formats supported are abi, scf and seq (or FASTA). Chromatograms of the assembled sequences are displayed in a synchronized format with the generated contig. Ambiguous bases in the contig are highlighted and corrections are suggested by rnaBaser based on Quality Values of the trace files. Minimum input from the user required. Editing of ambiguous bases, including insertion and deletion, is possible. The settings of the assembly engine can be adjusted by the user.

The user can personalize the appearance of chromatograms, nucleotides, background. The Quality Values of the trace files are displayed above chromatograms, so that the user can easily decide on the corrections in the final contig. The original chromatogram files will be trimmed automatically based on Quality Values.

The contig is automatically saved in FASTA format, in the same directory with the original trace files. By using a built-up database of primer and vector sequences, that can be edited/upgraded by the user, rnaBaser can be set to automatically trim the vector sequence out of the final contig.