RNAsnp webserver::Template

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

Template program

The Perl template program can be used to access several of the web services and parse the output data.
Download: rnasnp.pl

Usage

./rnasnp.pl -f <seq_file> -s <snp_file> [OPTIONS]

Details

The input fields given in the submit page can be accessed with the following options:

Flag	Data type	Value	Field Name
-f	STRING	File	Input sequence
-s	STRING	File	SNP details
-m	INT	1 or 2 or 3 (default='1')	Mode of operation 1 - based on global folding (using RNAfold) 2 - based on local folding (using RNAplfold) 3 - to screen putative structure-disruptive SNP
-w	INT	200 to 800 divisible by 50 (default='200')	Folding window: size of flanking regions on either side of SNP
-c	FLOAT	0.01 to 0.05 (default='0.01')	Cut-off for the base pair probabilities
Additional options
Parameters associated with (mode) -m 1:
-M	INT	1 or 2 (default='1')	Measures: 1 - distance; 2 - Correlation coefficient
-l	INT	50 to N (length of input sequence) (default='50')	Minimum length of the sequence interval
Parameters associated with (mode) -m 2:
-W	INT	200 to 300 (default='200')	Average the pair probabilities over windows of size
-L	INT	120 to 150 (should not be > W-50) (default='120')	Maximum allowed base pair span
-X	INT	20 to 30 (default='20')	Length of the local structural element that we expect to have an effect
-Y	INT	120 to 150 (should not be > -L) (default='120')	Length of the interval over which the local structural changes are evaluated (default='120')
Parameters associated with (mode) -m 3:
--pvalue1	FLOAT	0 to 1 (default='0.1')	P-value threshold to filter SNPs that are predicted using mode 2
--pvalue2	FLOAT	0 to 1 (default='0.05')	P-value threshold to filter SNPs that are predicted using mode 1
-e	INT	200 to 800 (default='200')	Minimum length of flanking regions on either of SNP

Please refer the help page to get more details about each field. The default value assigned for these fields under "Additional options" section are the optimal values that we found from the application of RNAsnp to known data sets. Moreover, the background distribution used for the calculation of empirical p-value was generated with these default values. Thus, the p-value approximation can deteriorate when these default values are changed to a greater extent.

Example

$ ./rnasnp.pl -f seq.txt -s snp.txt
Output:
Job Id: 6041-3098916775

SNP		Folding Window	Local region	distance	p-value	
T22G		1-222		15-64		0.2482		0.0518	
T22G-G17C	1-217		13-66		0.0700		0.3464	

The complete details of RNAsnp output is available in './RNAsnp_results_6041-3098916775.zip'

Download the example input files: seq.txt snp.txt