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RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure
Please fill out the submission form and click the
Submit
button given below. Input fields marked with a
*
are required.
(
Load Example Data
)
Input sequence*
Enter your input sequence here in either fasta format or linear sequence (without gaps).
[?]
(or) Upload sequence file:
(or) Select sequence from genome database
Clear
Mammal
Vertebrate
Deuterostome
Insect
Worm
Other
Human
Chimp
Gorilla
Orangutan
Gibbon
Rhesus
Baboon
Squirrel monkey
Marmoset
Tarsier
Mouse lemur
Bushbaby
Tree shrew
Mouse
Rat
Kangaroo rat
Naked mole-rat
Guinea pig
Rabbit
Squirrel
Pika
Pig
Alpaca
Dolphin
Sheep
Cow
Horse
Cat
Dog
Panda
Microbat
Megabat
Hedgehog
Shrew
Elephant
Rock hyrax
Tenrec
Manatee
Armadillo
Sloth
Opossum
Tasmanian devil
Wallaby
Platypus
hg19
hg38
hg18
genome
region
SNP details*
Enter your SNP details in the required format
[?]
XposY
,
X
is the wild-type nt.,
Y
is the mutant and
pos
is the position
of nt. (pos=1 for first nucleotide in a sequence)
In case of multiple SNPs, separate each SNP with hypen "-"
More than one SNP to test in a single run, provide them in seperate lines
chrNN:XposY
, where
NN
is chr. number,
X
is the wild-type nt.,
Y
is the mutant and
pos
is the position of nt.
More than one SNP to test in a single run, provide them in seperate lines
(or) Upload SNP file:
Job options
Enter your e-mail adress if you want to receive a notification after the job has finished, and give your job any custom name.
E-mail
Job name
Mode
Select the mode of operation
[?]
Mode 1 - based on global folding (RNAfold)
[?]
Mode 2 - based on local folding (RNAplfold)
[?]
Mode 3 - to screen putative structure-disruptive SNP
[?]
Folding window
Select the size of flanking regions on either side of SNP
[?]
100
150
200
250
300
350
400
450
500
550
600
650
700
750
800
Select the size of flanking regions on either side of SNP
[?]
200
250
300
350
400
450
500
550
600
650
700
750
800
Additional options
Parameters associated with mode 1
[?]
Measure
distance
Correlation coefficient
Minimum length of the sequence interval
Cut-off for the base pair probabilities
Parameters associated with mode 2
[?]
Average the pair probabilities over windows of size
Maximum allowed base pair span
Length of the local structural element that we expect to have an effect
Length of the interval over which the local structural changes are evaluated
Cut-off for the base pair probabilities
Parameters associated with mode 3
[?]
P-value threshold to filter SNPs that are predicted using Mode 2
P-value threshold to filter SNPs that are predicted using Mode 1
Minimum length of flanking regions on either of SNP
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