RNAsnp Web Server::Example

RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure

The three different modes of RNAsnp is demonstrated with the following examples:

Example 1: For a user given input sequence and SNP, the effect on local region of RNA secondary structure was predicted using Mode 1.
Example 2: For the same input sequence and SNP of example 1, the effect on local region of RNA secondary structure was predicted using Mode 2.
Example 3: A genomic region from hg19 assembly of human genome was selected to screen the putative structure-disruptive SNPs using Mode 3.

Example 1

Input sequence

The input sequence in fasta format

>gi|56682960|ref|NM_000146.3| Homo sapiens ferritin, light polypeptide (FTL), mRNA
GCAGTTCGGCGGTCCCGCGGGTCTGTCTCTTGCTTCAACAGTGTTTGGACGGAACAGATCCGGGGACTCT
CTTCCAGCCTCCGACCGCCCTCCGATTTCCTCTCCGCTTGCAACCTCCGGGACCATCTTCTCGGCCATCT
CCTGCTTCTGGGACCTGCCAGCACCGTTTTTGTGGTTAGCTCCTTCTTGCCAACCAACCATGAGCTCCCA
GATTCGTCAGAATTATTCCACCGACGTGGAGGCAGCCGTCAACAGCCTGGTCAATTTGTACCTGCAGGCC
TCCTACACCTACCTCTCTCTGGGCTTCTATTTCGACCGCGATGATGTGGCTCTGGAAGGCGTGAGCCACT
TCTTCCGCGAATTGGCCGAGGAGAAGCGCGAGGGCTACGAGCGTCTCCTGAAGATGCAAAACCAGCGTGG
CGGCCGCGCTCTCTTCCAGGACATCAAGAAGCCAGCTGAAGATGAGTGGGGTAAAACCCCAGACGCCATG
AAAGCTGCCATGGCCCTGGAGAAAAAGCTGAACCAGGCCCTTTTGGATCTTCATGCCCTGGGTTCTGCCC
GCACGGACCCCCATCTCTGTGACTTCCTGGAGACTCACTTCCTAGATGAGGAAGTGAAGCTTATCAAGAA
GATGGGTGACCACCTGACCAACCTCCACAGGCTGGGTGGCCCGGAGGCTGGGCTGGGCGAGTATCTCTTC
GAAAGGCTCACTCTCAAGCACGACTAAGAGCCTTCTGAGCCCAGCGACTTCTGAAGGGCCCCTTGCAAAG
TAATAGGGCTTCTGCCTAAGCCTCTCCCTCCAGCCAATAGGCAGCTTTCTTAACTATCCTAACAAGCCTT
GGACCAAATGGAAATAAAGCTTTTTGATGCA

Input SNP

T22G

Output of Mode 1

Graphic summary

The local region detected with maximum structural change is colored according to the p-value. If the p-value is greater than 0.2 (i.e not so significant structural change) the region is colored in black.

U22G

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Description

SNP	Folding Window	Local region	distance	p-value
U22G	1-222	15-64	0.2482	0.0518

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Structure Details

U22G

Base pair probabilities of the local region 15-64

The upper and lower triangle of the matrix represents the base pair probabilities of wild-type and mutant sequences, respectively.

Download: PS | PDF| TXT

Base pair probabilities of the global sequence (1-222) considered for folding: PS | PDF| TXT

(The base pair probabilities of the local region represented above was a subset taken from the global base pair probabilities)

The optimal secondary structure of global wild-type sequence (1-222)*:
minimum free energy = -66.80 kcal/mol

Download: PNG | EPS

The optimal secondary structure of global mutant sequence (1-222)*:
minimum free energy = -62.80 kcal/mol

Download: PNG | EPS

*The structure shown here is used only for visualizing the secondary structure in planar graph representation.

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Example 2

The input sequence and SNP of Example 1 was used here to predict the structural effect using Mode 2

Output of Mode 2

Graphic summary

U22G

Download

Description

SNP	Folding Window	Local region	distance	p-value
U22G	1-222	11-66	0.2165	0.0348

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Structure Details

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Example 3

The sequence from the genomic region chr19:49468565-49469565 from hg19 assembly of human genome was selected to screen the putative structure-disruptive SNPs (p-value < 0.05) using Mode 3.

Visualizing the predicted putative structure-disruptive SNPs in UCSC genome browser

The first two tracks are RNAsnp-specific. The first track represents the chromosomal location of the structure-disruptive SNPs and the second track represents the local region where the maximum structural change was observed due to these disruptive SNPs.Click here to visualize output in UCSC genome browser