Ohayon-Sequencer

A user friendly interface for sequencing DNA along with tools for sequence manipulation and base pairing analysis.

Features include:

• Sequencer Reverse/Complement converted
• Ability to sequence Loop DNA
• Ability to find strongest base pairing configuration between two strands

Frontend: React JS/Flux Dependancy Management: Webpack Backend:NodeJS/Express/Java

NOTE: Must use Node version 6.9.4 or Node@6 (homebrew)

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Future Updates will include:

• Desired DNA melting points for strand components

Testing:

1. Go to console and enter "npm run server"

2. On web browser go to localhost:3000

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Questions: Email [email protected]

Literature Cited:

1. Allawi HT, SantaLucia J Jr. 1997. Thermodynamics and NMR of internal G−T mismatches in DNA. Biochemistry 36:10581–94

2. Allawi HT, SantaLucia J Jr. 1998. Nearestneighbor thermodynamics of internal AC mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435–44

3. Allawi HT, SantaLucia J Jr. 1998. Nearestneighbor thermodynamics parameters for internal GA mismatches in DNA. Biochemistry 37:2170–79

4. Allawi HT, SantaLucia J Jr. 1998. Thermodynamics of internal C-T mismatches in DNA. Nucleic Acids Res. 26:2694– 701

5. Antao VP, Lai SY, Tinoco I Jr. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19:5901–5

6. Antao VP, Tinoco I Jr. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.Nucleic Acids Res. 20:819–24

Developed in the NYU DNA Nanotechnology Lab. Contributors: Samuel Mao, Meet Barot