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Picky   Picky: Optimal Oligonucleotide Design and Analysis

Picky 2 Oligo Microarray Design Oligo Sets
C. elegans
E. coli
Plasmodium falciparum

Picky 1 Oligo Microarray Design Oligo Sets


Oligo Microarray Design Tutorials
Guided Tour
Animated Tutorial

Gene Assembly
Microarray Calibration
shRNA Design

Change Log

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PICKY is a software tool for selecting optimal oligonucleotides (oligos). PICKY allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. PICKY can also be used to analyze existing microarray probes and evaluate their design quality. Because PICKY uses rigorous whole genome-based thermodynamic screening to identify potential hydrogen binding sites of each probe, it can also be utilized to design short interference RNA (siRNA) for gene knockout applications and to discover possible targets of regulatory short RNAs (e.g., microRNAs or sRNAs). Picky has exceptional computational capability and is also user friendly. Macintosh, Unix and PC versions are all available. The 32-bit Picky is free to all users under a non-exclusive free license. Academic and government users can also obtain free 64-bit Picky license for nonprofit use. Commercial licenses are separately available for 64-bit Picky.

Announcing Picky 2.2!

Picky 2.2 includes several important new features:

  1. New 64-bit Picky version is finally available to analyze ever bigger genomes and gene sets.
  2. Fully multi-threaded implementation to take advantage of all computing cores available to Picky.
  3. New extended output file format to report more potential nontargets for each probe designed or analyzed.
  4. Numerous user interface, usability and online help improvements to help make the best use of Picky.

For a comprehensive list of the various new features added to Picky 2.2, check out its Change Log.

Note that all Picky reference oligo sets provided on this website were previously created using Picky 2.0 and are out of date; it is strongly recommended that the new Picky 2.2 be used to redesign any production oligo sets you might wish to use for actual experiments.

How to download Picky 32-bit versions (free to all!)

  1. Input your email and optional information into the boxes at the bottom of the Registration page.
  2. Submit your registration. You should be taken to a confirmation screen that will refresh back to this page shortly.
  3. Check your email inbox in a moment. You should get an email from our automatic account service with a new password. If you do not receive this email, it may have been trapped by your spam filter. Check your spam email bin for this account email before you contact us.
  4. Go to the Download page and input your username and password to download Picky 32-bit version. Your username is the email you registered with us and the password is the one you obtained in the account creation email.
  5. Click on "Submit" button and you will be taken to the download page where you can download Picky 32-bit versions for various platforms.

How to obtain Picky 64-bit versions

  1. If you are a commercial user and wish to license the 64-bit Picky for commercial use, please visit the Iowa State University Research Foundation Technology Details Page for Picky and contact the listed License Associate there for Picky commercial licenses.
  2. If you are an academic, government or other nonprofit user and wish to obtain the 64-bit Picky, please see instructions in the bottom of the download page.


Two tutorials were developed to help users better understand Picky. These tutorials introduce the features of Picky 2.0 and better acquaint users with its functionality. Users can quickly gain first hand experience of Picky and begin oligo design after completion of these tutorials:

Picky Guided Tour: Acquaints users with a thorough explanation of Picky user interface and functionality. [Download PDF Version]

Picky Animated Tutorial (Flash): Demonstrates step-by-step guide to Picky functionality using a sample Arabidopsis File from GenBank.

Related Papers

If you find Picky useful to your research, please cite the Picky papers below that are most relevant to your work. If you have no preference, we recommend you cite the newest Shared Probe Design paper.

Shared probe design and existing microarray reanalysis using PICKY.
Chou HH.
BMC Bioinformatics. 2010 Apr 20;11:196.PMID: 20406469

Direct calibration of PICKY-designed microarrays.
Chou HH, Trisiriroj A, Park S, Hsing YI, Ronald PC, Schnable PS.
BMC Bioinformatics. 2009 Oct 23;10:347.PMID: 19849862

Picky: oligo microarray design for large genomes.
Chou HH, Hsia AP, Mooney DL, Schnable PS.
Bioinformatics. 2004 Nov 22;20(17):2893-902. Epub 2004 Jun 4.PMID: 15180932


The Picky development benefits from a recent NSF research grant support the development of a new siRNA design software which is related to Picky. This grant partially supports the efforts to revise Picky for 64-bit computing and to make the 32-bit Picky freely available to the public. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Questions & Comments

Please send all questions, bug reports, commercial license inquiry and wish lists to Note that you must register your email first so your emails will not be filtered out as spams.

Last modified June 13, 2008 . All rights reserved.

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