License Plates : automated short RNA nomenclature

Manual Decoding and Encoding of License Plates

Encoding and decoding a license plate is easy. You can download and use the license plate code locally. If you prefer to manually encode and decode a license plate you can do so following the instructions and table below.

How to Encode a License Plate

To encode a license Plate:

• Divide the sequence to portions of five (as many as you can) and any portion that's leftover.
• Search the triplets below for a triplet that has the "portion sequence" in the middle, for each of your portions.
• Combine the third part of the triplet in the order of the portions to get the encoded sequence. For encoding, you never need the first part.
• Add your molecule type and the sequence length to get the licence plate.

For example, let's say we want to encode AAGACTTTTTCTCTGAC. This is a GRCh37 3'-tRF from tRNA^ProTGG whose licence plate is tRF-17-DDZZ4Y1.

• We divide in as many portions of 5 we can and a leftover portion. The portions are "AAGAC", "TTTTT", "CTCTG" and "AC".
• We find the triplets that contain the sequence of the portion in the middle. Those are "5 AAGAC DD", "5 TTTTT ZZ", "5 CTCTG 4Y", and "2 AC 1".
• We combine the third part of each triplet to get DDZZ4Y1.
• We add "tRF" and "17", the type and length to get trf-17-DDZZ4Y1.

How to Decode a License Plate

To decode a license plate:

• Divide the license plate to three parts, the molecule type, the length and the encoded sequence.
• Divide the length with 5 and keep the integer part of the division (quotient). If it divides exactly, you will retrieve as many as the quotient portions from the table. If there is a remainder (if length - quotient * 5 is not zero, the result is the remainder), you will retrieve as many as the quotient plus one for the remainder.
• Divide the encoded sequence to couples of letters. If the last one has only letter it's fine.
• Retrieve the triplets from the table below as follows. Retrieve triplets whose first component is 5 and the last is the corresponding couple of letters, as many times as the quotient. Retrieve a triplet that starts with the remainder and the last is the last couple of letters (or one letter).
• Combine the middle component of the triplets (in the order of retrieval) to get the molecule sequence.

For example, to decode tRF-17-DDZZ4Y1.

• The three parts of the license plate are type "tRF", length "17", and encoded sequence "DDZZ4Y1".
• If we divide 17 by 5 we get, 3.4, 3 is the quotient. To get the remainder we calculate 17 - 5*3 = 2. So the remainder is 2.
• If we divide the encoded sequence to couples we get, "DD", "ZZ", "4Y", and "1". It's fine if the last is only one letter.
• We retrieve from the table, 4 triplets. 3 that start with 5 and the last component is the corresponding couple and 1 that starts with 2 and the last component is the last letter (or couple). Those are, "5 AAGAC DD", "5 TTTTT ZZ", "5 CTCTG 4Y", and "2 AC 1".
• We combine the middle parts to get, AAGACTTTTTCTCTGAC.

Table of encoding/decoding