easy Primer Design

easy Primer Design

About this app

easy Primer Design is a tool that helps you to design your PCR primers anywhere in a time efficient manner: at the bench while waiting for an experiment, at your way to, or from work, or at the office. Simply paste your nucleotide sequence and specify your requirements to generate primer sequences for your PCR cloning application.

Features:
-Use the paste button to enter your sequence. The entered CDS/sequence contains numbers, spaces, line breaks, upper, or lower case letters? It doesn't matter! easy Primer Design removes numbers, spaces, and line breaks and changes everything to upper case letters!
-enter your sequence without start and stop codon (and get a warning message if you did forget to remove one of it) to be flexible for primer design for plasmids with N-terminal or C-terminal tags.
-choose from more than 20 different restriction enzyme sites, Golden Gate cloning is supported via BsaI and BsbI, you can even enter the overhang
-get Warning messages if your chosen enzyme would cut your entered sequence
-maximum flexibility via the restriction enzyme option 'other', enter your restriction enzyme site if its not in the list - non-palindromic sequences are supported! If your entered restriction site is present in your entered sequence or in its reverse complement you'll get a warning message!
-get a warning message to avoid common 'copy-paste' errors, if your entered sequence contains an incomplete codon!
-include a KOZAK sequence in the forward primer if you want one
-choose if you need a Start codon, and if you need a Stop codon (all 3 common stop codons are selectable)
-enter a melting temperature for your primers, its calculated using the salt adjusted melting Temperature
-enter the salt concentration (Na+)
-enter a 5'-end extension for both of your primers
-primers are generated to end with G or C
-melting Temperature, G/C content and primer length are displayed
-transparent designing process! all intermediate steps are displayed! Your selected options are displayed under the final results!
-copy button to copy the entire output and sent it via e-mail to your desktop PC for the next design steps or save it as a file!
-Version 0.03 update: new feature 'DeletionIn': helps you to design primers for overlap extension PCR to delete specific internal regions from a sequence (e.g. delete domains)
-Version 0.045 update: new feature 'Mutation' helps you to design primers for overlap extension PCR to mutate a specific codon in your sequence to code for another amino acid
-Version 0.060 update: new feature: 'DeletionNC' - helps you to design primers to delete N(5')- or C(3')-terminal regions from your sequence
-Version 0.080 update: new feature: 'Insertion' - swipe left in the top main menu and find help for designing primers for overlap extension PCR to insert an insert-sequence into your sequence
- Version 0.085 update: new Feature: 'Replace' - swipe left in the top main menu to get help for designing primers for overlap extension PCR, that replace an internal region with an entered insert-sequence

Please note: easy Primer Design mobile app does not deliver ready-to-use primer sequences it only supports you during the process of primer design. The user has to validate the correctness of every part of the generated result carefully and carry out all other necessary tests!

Happy cloning! -Hope it helps :)

What's new

-New Feature: Replace - swipe left in the top main menu to get help for designing primers for overlap extension PCR, that replace an internal region with an entered insert-sequence
-help section updated