Cross-Hybridization Analysis Network of Gene Expression
 --  Cross-Hybridization Based Oligonucleotide Probe Design

Species

Homo sapiens
Mus musculus
Saccharomyces cerevisiae

Input UniGene cluster ID (such as Hs.1311), gene symbol (such as CD1C), or yeast ORF (YAL007C):



Probe Picking Options

Maximum Probe Number to Return:

Probe Length: Min: Max:

Probe Tm: Opt: Range(+/-):

Maximum Poly A or T in Each Oligo Picked:

Maximum Poly G or C in Each Oligo Picked:

Content Window Size:

Maximum A and T Content in Window:

Maximum G and C Content in Window:

Maximum Self-Complementarity (Palindrome) Score:

Oligo Concentration(nM):

Salt Concentration(mM):

Affymetrix Probe Selection Rules for 20-mer Probes

Total number of As or Ts less than 10

Total number of Cs or Gs less than 9

Number of As or Ts in any window of 8 bases less than 7

Number of Cs or Gs in any window of 8 bases less than 6

No more than 5 Cs or Gs in a row

No more than 6 As or Ts in a row

A palindrome score is less than 7

Lockhart et al.(1996) Expression monitoring by hybridization

to high-density oligonucleotide arrays. Nat. Biotechnol. 14,

1675-1680


This tool is an application of the Featurama program,which is written by David Shteynberg.(http://probepicker.sourceforge.net/)