FASTSNP User's Guide

This user guide explains how to use FASTSNP. Please refer to FAQ if you need quick answers. To learn about how FASTSNP works, please read the document.

Brief Introduction

FASTSNP provides SNP prioritization services based on the information collected from the Internet at query time. You can click on "Demo" to see an example of SNP prioritization results by FASTSNP.

FASTSNP provides three options for you to submit requests. If you already have some candidate SNPs on a candidate gene, you may use "Query by Candidate Gene" to select the specific SNPs on the gene to perform prioritization.  If you have a specified SNP or a list of SNP rsid's needs to be prioritized, you can use "Query by SNP" option and upload your SNP list in an Excel-format file. Finally, if you have a novel SNP sequence, FASTSNP provides Novel SNP analysis for you. FASTSNP will generate a SNP Function Report for each SNP. You can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information. For detailed explanation of each step, we encourage you to read the followings:

SNP Potential Functional Effect

FASTSNP prioritizes SNPs according to twelve phenotypic risks and putative functional effects, such as changes to the transcriptional level, pre-mRNA splicing, protein structure, etc. A unique feature of FASTSNP is that the prediction of functional effects is always based on the most up-to-date information, which FASTSNP extracts from eleven external Web servers at query time using a team of re-configurable Web wrapper agents. The potential functional effects on the phenotype include alterations in:

¨            the premature translation termination (nonsense; stop codon gained),

¨            the exons that cause an amino acid change (non-synonymous),

¨            the splicing sites,

¨            the transcription factor binding sites at promoter regions,

¨            the exonic splicing enhancer motifs,

¨            the exonic splicing silencer motifs,

¨            and the 3utr post-transcriptional regulatory region.

Getting Start for SNP Prioritization

Step1: Search Gene l        Start to select candidate SNPs using the Query by Candidate Gene by gene symbol. There are two other ways allow you to select SNPs. 1) Input a SNP's rsid or upload a rsid list of SNPs in an Excel file for batch analysis. 2) Paste your Novel SNP sequence.

Step2: Select Transcript l           Click Transcript "Button" to retrieve a SNP set in a gene

Step3: Filter SNP Set You can filter your SNPs to refine your SNP set by region, allele frequency, and validation status. You may select multiple SNP rsid's and click “Launch” button to perform SNP prioritization. l           Check SNP on the SNP rsID column l           Click "Launch" button for SNP prioritization

Step4: Start SNP prioritization Each time you start SNP prioritization, the system will assign a Task Id. You may send the link to your email address or view SNP Prioritization Result by clicking on the link. l           Send the task link to your email address l           Click on the link to open SNP Prioritization Result

Step5: SNP Risk Ranking This page lists all SNPs ordered by their particular risk ranking. FASTSNP gives you the putative functional effects for each SNP. Clicking on the button in the SNP rsid column will open a detailed SNP Function Report. l           SNP Prioritization Result will list SNP with its risk ranking and possible function types l           Click each SNP rsid button to open SNP Function Prediction Report

Step6: View SNP Function Report l           SNP Function Prediction Report shows the phenotypic changes by SNP alleles

Always Up-to-Date Feature

A unique feature of FASTSNP is that the prediction of functional effects is always based on the most up-to-date information, which FASTSNP extracts from eleven external Web servers at query time using a team of re-configurable Web wrapper agents. These Web wrapper agents automate Web browsing and data extraction and can be easily configured and maintained with a tool that uses a machine learning algorithm for text mining. This allows users to configure/repair a Web wrapper agent without programming.