Molecular structures
.pdb, .cif, .mmcif, .sdf, .mol, .mol2 and .xyz files open as an interactive 3D structure. BioBase parses each file by its extension and reads .cif and .mmcif as mmCIF. If the contents don’t match the extension, the viewer reads: “This structure could not be displayed. Check that the file matches its format.”Sequences
.fa, .fasta, .fna, .ffn, .faa and .frn files open in the sequence viewer. BioBase detects the alphabet from the residues. The header shows it with the length and, for DNA and RNA, the GC content, for exampleDNA · 12,345 bases · 41.2% GC.
DNA and RNA open as a linear map and switch to a circular map with Circular view. Protein has the linear map only. DNA also shows the complement strand.
The viewer shows the first record of a multi-record file, up to 250,000 residues. When it shows less than the whole file, it reads “Showing the first of N records.” or “The displayed record is limited to 250,000 residues.”
A file with no residues reads: “This sequence file does not contain a readable residue record.”
FASTQ and GenBank files open as text in the editor.