Biochemistry

Build DNA, RNA and peptides from a sequence, FASTA or HELM, work with monomers, transform sequences, align them and draw plasmid maps.

1. 1 · How-toHow to build a peptide, DNA or RNA from its sequenceChoose Insert › Build from sequence…, type the one-letter sequence, pick Peptide, DNA or RNA and Residues or Full structure, and press Insert.
2. 2 · How-toHow to open a HELM stringPress / for Quick insert, paste a HELM string such as PEPTIDE1{A.C.D.E}$$, and choose Build from HELM. The sequence builder opens with it; press Insert.
3. 3 · How-toHow to browse and add monomersChoose Object › Chemistry › Monomers. Switch between Peptide, Nucleotide and Chemical, search by id or name, and add your own with an id and a SMILES with attachment points.
4. 4 · How-toHow to align two sequencesSelect two sequences, or open Object › Chemistry › Align two sequences and paste two sequences or two FASTA records. Press Align to see the identity, gaps, score and the aligned pair.
5. 5 · How-toHow to draw a plasmid mapChoose Insert › Plasmid map…, paste a sequence, FASTA or GenBank (or Paste an example), pick Circular or Linear, check the Map, Sites and Primers tabs, and press Insert the map.