Sequence Input File Format

Staple and scaffold sequences are input into REVNANO using a plain text file with extension .rev.

You can see the Paper Examples page for many example sequence input files.

The sequence input file has a simple format:

  • Comments can be included at any point in the text file by using the symbol #. A comment occupies the entire line it is on.

  • A keyword LINEAR or CIRCULAR may occur on a separate line anywhere in the text file, and denotes if the scaffold is a closed loop or not. This is most conveniently placed after the scaffold sequence. If this keyword is not specified, the scaffold defaults to LINEAR.

  • The first nucleic acid sequence encountered in the text file is considered as the scaffold sequence, listed 5’ to 3’.

  • Subsequent sequences in the text file are considered as staple sequences, each listed 5’ to 3’.

Note

  • * pairs must be put around staple sequence regions which are dangles or interior staple loopouts (regions not designed to hybridise with the scaffold). For example: Staple *TTTT*AAATCA*TTTTT*GGTCTTTACCCTGACGATTAGAG*TTTT* has a TTTT dangle at both ends marked, and a TTTTT interior staple loopout region marked.

  • Sequences can written in upper or lower case, or a mixture of both

  • Sequences will have internal spaces automatically removed

  • One sequence per line: Sequences split over multiple lines are treated as separate sequences