OligoDesign: LNA spiked oligonucleotide design for expression arrays
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Ver. 1.2, 2002-11-14
Design oligonucleotides for expression arrays
user instructions
documentation
databases
The sequence of the target gene:
Options
Advanced options
database
h_sap_gene
h_sap_genome
m_mus_gene
m_mus_genome
r_nor_gene
r_nor_genome
a_tha_gene
a_tha_genome
d_mel_gene
d_mel_genome
c_ele_gene
c_ele_genome
p_tro_gene
p_tro_genome
s_cer_genome
length of the oligonucleotide
8 - 300
DNA only
LNA frequency
0 - 300
LNA phase
0 - 300
LNA end length
0 - 300
min. dist. between oligonuc.
0 - 300
min tm
0 - 100
max tm
0 - 100
max. match %
1 - 100
max. stretch %
1 - 100
position preference
anywhere
3'
5'
blast word length
7 - 50
blast expectation cutoff
0 - 10000
blast search strand
both strands
direct only
reverse only
weight of max. match
0
1
2
3
4
5
weight of max. stretch
0
1
2
3
4
5
weight of self. hyp.
0
1
2
3
4
5
weight of sec. struct.
0
1
2
3
4
5
weight of target sec. struct.
0
1
2
3
4
5
weight of Tm
0
1
2
3
4
5
weight of position preference
0
1
2
3
4
5
id = 1283595590209