Grasshopper

algorithmic modeling for Rhino

Alba

ADDON

Component Index > Alba

Library
Utilities
Visualize
Transcription/Translation
Digest
Ligate
Protein

Library

BioBrick Categories of Parts
Provides a list of part categories for inputinto the BB Library
BioBrick Prefix and Suffix Adder
Contains a cluster of Grasshopper components
BioBricks Library
library of all the parts in the BioBricks registry.
BioBricks Prefix Standard
simply the sequence of the standard BioBricks prefix used to enable ligation with compatible sticky ends
BioBricks Prefix ATG
simply the sequence of the standard BioBricks prefix used, with sequences starting with ATG, to enable ligation with compatible sticky ends
BioBricks Suffix
simply the sequence of the standard BioBricks suffix used to enable ligation with compatible sticky ends
E0240 GFP with RBS, and Terminator
RBS: B0032 +
GFP Reporter: E0040 +
Terminators: B0010 & B0012
GFP with Promoter, RBS, and Terminator
Tet Promotor R0040 +
RBS: B0034 +
GFP Reporter: E0040 +
Terminators: B0010 & B0012
Plasmid Backbones DNA
Provides the DNA for teh 4 commonly use BioBrick backbones.
Plasmid Insert
Insert a gene into a plasmid backbone, optionall add in the BB prefix and suffix. Index reamins at beginning of gene; the prefix is at the end of the sequence.
Promoter DNA
Provides a list of the 10 most commomnly used BioBrick promoters, and outputs the DNA of the selected part.
Protein Coding DNA
Provides a list of the 10 most commomnly used BioBrick protein codeing sequences, and outputs the DNA of the selected part.
Resistance to Chloramphenicol
DNA sequence to produce Chloramphenicol resistance
Resistance to Kanamycine
DNA sequence to produce Kanamycine resistance
Resistance to Tetracycline
DNA sequence to produce Tetracycline resistance. On BioBrick plasmid backbone pSB1T3 this gene is on the primary strand.
Resitance to Amp
DNA sequence to produce Ampicillin resistance
RFP with RBS, and Terminator
RBS: B0034 +
RFP Reporter: E1010 +
Terminators: B0010 & B0012
Ribosome Binding Site DNA
Provides a list of the 10 most commomnly used BioBrick RBS, and outputs the DNA of the selected part.
Teminator DNA
Provides a list of the 10 most commomnly used BioBrick terminators, and outputs the DNA of the selected part.
YFP with RBS, and Terminator
RBS: B0034 +
YFP Reporter: E0030 +
Terminators: B0010 & B0012

Utilities

Complementary Strand
creates a complementary strand based in the input sequence
DNA Clean
gets rid of anything that is not a, A,T,G, or C and capitalizes all characters
DNA Find
Finds a sequence within a sequence and return the domain of its location.
Primer Design
to find a primer with good melt temp and GC content and avoiding bad hairpins
Random DNA
create a ramndom string of GTAC
Reverse DNA
reverses the sequence of DNA
Reverse Subdomain
reverses the position and direction of a subdomain

Transcription/Translation

E. coli Optimization
create an optimized RNA sequence for E coli to produce the input AA chain.
Simple Transcription
simple conversion DNA to RNA changing T to U
Simple Translation
converts RNA into Amino Acids
Transcription Promoter to Terminator
Transcribes DNA to RNA starting just after the promoter site and ending just prior to the termitator site
Transcription σ
Converts DNA to RNA based on -35 and -10 sites
Translation
Translates RNA to amino acid chain with options for finding the proper reading frame

Protein

PDB Sort
sort protein data base file
PDB Open
make the pdb info accessible
PDB Plot
create a visual energy plot of a pdb file
Protein Query
Search the RCSB Protein DataBase for matching Amino Acis sequences and the address of a corresponding .pdb file.
Protein Ribbon
visualizes the structure of a protein

Visualize

Amino Acid Visualizer
Creates and displays an offset complementary strand
DNA Subdomain Visualizer
Visualizes the specified subdomain of a strand
DNA Complementary Strand Visualizer
Creates and displays an offset complementary strand
DNA Complementary Subdomain Visualizer
Visualizes the specified subdomain of a created offset complementary strand
DNA Visualizer
Visualizes the DNA in the Rhino viewport

Ligate

A Simple Ligation
Concatenates two DNA sequences
Ligate
Ligate tests to see if 2 strands have matching sticky ends. Is sothey are joined together. If both ends connect, plasmid is set to true.
Sticky Ends
identifies the overhanging ends of DNA.

Digest

Enzyme List
A list of enzymes to choose from that passes the proper index for the Restriction Enzymes output object
Restriction Enzyme Digest
Cuts up DNA based on target sits of the input restriction enzyme and outputs double stranded DNA with sticky ends.
Restriction Enzymes Cut Locations
outputs the cut locations of any major restriction enzyme. use the Enzymes List to choose the enzyme you want or enter the index if you know it already

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