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Quartz Syncer
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‎content/dscode.md‎

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@@ -31,50 +31,49 @@ However, they do not address the single or double strandedness of DNA.
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The dscode alphabet is a super set of the IUPAC alphabet. The symbols take on a different meaning as each symbol represent a base pair (a base in a DNA strand and its complementary base on the other strand) instead of a single base.
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The alphabet uses an additional ten symbols to represent single stranded regions where there is no complementary base (see table below). Dscode remains 100% backward compatible with the IUPAC alphabet. [link](https://docs.google.com/document/d/1QAjGeCByWemjVZnva7ap3sg7e8wIwVUK4-pIjt4GIZ0/edit?usp=sharing)
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| Alphabet | Symbol | Complement | Bases | dsIUPAC extended meaning |
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| ---------- | ------ | ---------- | ------------------------------------------- | ------------------------ |
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| IUPAC | G | C | G | G/C |
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| " | A | T | A | A/T |
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| " | T | A | T | T/A |
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| " | C | G | C | C/G |
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| " | R | Y | G or A | R/Y |
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| " | Y | R | T or C | Y/R |
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| " | M | K | A or C | M/K |
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| " | K | M | G or T | K/M |
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| " | S | S | G or C | S/S |
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| " | W | W | A or T | W/W |
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| " | H | D | A or C or T | H/D |
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| " | B | V | G or T or C | B/V |
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| " | V | B | G or C or A | V/B |
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| " | D | H | G or A or T | D/H |
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| " | N | N | G or A or T or C | N/N |
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| **dscode** | U | O | U in top strand, A in complementary strand | U/A |
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| " | O | U | A in top strand, U in complementary strand | A/U |
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| " | E | F | A in top strand, complementary strand empty | A/◻ |
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| **"** | I | J | C " | C/◻ |
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| **"** | P | Q | G " | G/◻ |
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| **"** | X | Z | T " | T/◻ |
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| **"** | Z | X | A in complementary strand, top strand empty | ◻/A |
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| **"** | Q | P | C " | ◻/C |
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| **"** | J | I | G " | ◻/G |
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| **"** | F | E | T " | ◻/T |
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| " | ! | A | A in upper strand A in lower strand | A/A |
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| " | # | C | A in upper strand C in lower strand | A/C |
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| **"** | $ | G | A in upper strand G in lower strand | A/G |
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| **"** | % | A | C in upper strand A in lower strand | C/A |
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| **"** | & | C | C in upper strand C in lower strand | C/C |
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| " | * | T | C in upper strand T in lower strand | C/T |
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| " | ( | A | G in upper strand A in lower strand | G/A |
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| **"** | ) | G | G in upper strand G in lower strand | G/G |
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| **"** | < | T | G in upper strand T in lower strand | G/T |
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| **"** | > | C | T in upper strand C in lower strand | T/C |
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| **"** | @ | G | T in upper strand G in lower strand | T/G |
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| **"** | : | T | T in upper strand T in lower strand | T/T |
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| **"** | ? | G | U in upper strand G in lower strand | U/G |
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| **"** | [ | C | U in upper strand C in lower strand | U/C |
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| **"** | ] | T | U in upper strand T in lower strand | U/T |
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| Alphabet | Symbol | Complement | Bases | dscode meaning |
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| ---------- | ------ | ---------- | ------------------------------------------- | -------------- |
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| IUPAC | G | C | G | G/C |
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| " | A | T | A | A/T |
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| " | T | A | T | T/A |
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| " | C | G | C | C/G |
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| " | R | Y | G or A | R/Y |
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| " | Y | R | T or C | Y/R |
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| " | M | K | A or C | M/K |
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| " | K | M | G or T | K/M |
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| " | S | S | G or C | S/S |
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| " | W | W | A or T | W/W |
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| " | H | D | A or C or T | H/D |
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| " | B | V | G or T or C | B/V |
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| " | V | B | G or C or A | V/B |
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| " | D | H | G or A or T | D/H |
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| " | N | N | G or A or T or C | N/N |
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| **dscode** | U | O | U in top strand, A in complementary strand | U/A |
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| " | O | U | A in top strand, U in complementary strand | A/U |
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| " | E | F | A in top strand, complementary strand empty | A/◻ |
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| **"** | I | J | C " | C/◻ |
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| **"** | P | Q | G " | G/◻ |
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| **"** | X | Z | T " | T/◻ |
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| **"** | Z | X | A in complementary strand, top strand empty | ◻/A |
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| **"** | Q | P | C " | ◻/C |
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| **"** | J | I | G " | ◻/G |
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| **"** | F | E | T " | ◻/T |
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| " | ! | A | A in upper strand A in lower strand | A/A |
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| " | # | C | A in upper strand C in lower strand | A/C |
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| **"** | $ | G | A in upper strand G in lower strand | A/G |
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| **"** | % | A | C in upper strand A in lower strand | C/A |
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| **"** | & | C | C in upper strand C in lower strand | C/C |
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| " | * | T | C in upper strand T in lower strand | C/T |
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| " | ( | A | G in upper strand A in lower strand | G/A |
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| **"** | ) | G | G in upper strand G in lower strand | G/G |
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| **"** | < | T | G in upper strand T in lower strand | G/T |
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| **"** | > | C | T in upper strand C in lower strand | T/C |
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| **"** | @ | G | T in upper strand G in lower strand | T/G |
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| **"** | : | T | T in upper strand T in lower strand | T/T |
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| **"** | ? | G | U in upper strand G in lower strand | U/G |
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| **"** | [ | C | U in upper strand C in lower strand | U/C |
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| **"** | ] | T | U in upper strand T in lower strand | U/T |
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The symbols PEXI and QFZJ that are not occupied by the extended IUPAC alphabet were adopted to imply single stranded DNA on either
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strand where no complementary bas exist.
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tAtUtCTAG
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PEXIaUaOaQFZJ representation using dsIUPAC
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PEXIaUaOaQFZJ representation using dscode
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```
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The choice of symbols for the dscode extension facilitate intuitive recognition of compatible single stranded regions, i.e. sticky-ends. The symbols that can anneal are adjacent in the alphabet eg. `Q-P`, `E-F`, `I-J`, only broken by X-Z due to necessity as Y is a parth of the IUPAC alphabet.
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```
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ASCII CAPS = ABCDEFGHIJKLMNOPQRSTUVWXYZ
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IUPAC = ABCD GH K MN RST VW Y
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dsIUPAC = EF IJ L OPQ U X Z + IUPAC
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dscode = EF IJ L OPQ U X Z + IUPAC
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punctuation = ! # $ % & * + ( ) < = > @ /: ' , - . ; ? [ \ ] ^ _ ` { | } ~ "
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```

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