What is FASTSNP?
What is FASTSNP?
What is the purpose of
FASTSNP? How does FASTSNP
predict a SNP's functional effects?
Which external Web servers are integrated in FASTSNP?
Where to get my SNP prioritization results?
Why there is no result for my SNP?
Why it takes so long to complete my request?
FASTSNP (Function Analysis and Selection Tool for Single Nucleotide Polymorphisms) is a web server that allows users to efficiently identify the SNPs most likely to have functional effects.
What is the purpose of FASTSNP?
FASTSNP prioritizes SNPs according to twelve phenotypic risks and putative functional effects, such as changes to the transcriptional level, pre-mRNA splicing, premature translation termination, and protein structure, etc. It allows users to select functional polymorphisms for association studies in a convenient way.
How
does FASTSNP predict a SNP's functional effects?
FASTSNP extracts from a variety of external bioinformatics Web servers at query time using a team of re-configurable Web wrapper agents. These Web wrapper agents automate Web browsing and data extraction. Please refer to the document of FASTSNP for more details . After information has been extracted, FASTSNP uses a decision tree to classify each SNP into a different phenotypic risk and ranks with a risk score.
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Table1. Definition and risk ranking of predicted functional effects of SNP by FASTSNP.
Coding Type Type Possible Effects Risk Ranking coding Non-sense Premature termination of amino-acid sequence Very high 5 Splicing Regulation (Abolished Protein Domain) Break exonic splicing enhancer binding site in coding sequence, leading to protein domain abolished Medium to high 3~4 Splicing Regulation (Same Protein Domain) Break exonic splicing enhancer / silencer binding site in coding sequence, containing same protein domains Low to medium 2~3 Mis-Sense (Non-conservative change) Change an amino acid in protein to one with different structure characteristics Medium to high 3~4 Mis-Sense (Conservative change) Change an amino acid in protein to one with similar or same structure characteristics Low to medium 2~3 Sense/synonymous Does not change amino acids in sequence Low 1 Untranslated Change untranslated region sequence No effect to low 0~1 Non-coding Promoter/regulatory region Does not change the amino acid, but can affect the level, location or timing of gene expression Low to medium 1~3 Upstream with no known function Change the upstream sequence without any known transcription factor binding site No effect 0 Intronic enhancer Alter a binding site of transcription factor in intronic region Low to medium 1~2 Intronic with no known function Change intronic sequence without any known funciton No effect 0 Splicing Site Break the consensuc splicing site sequence Medium to high 3~4 ¡@
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Which external Web servers are integrated in FASTSNP?
FASTSNP accesses eight Web servers that provide bioinformatics databases and analytical tools to predict functional effects for SNP prioritization, including NCBI dbSNP, Ensembl, TFSearch, PolyPhen, ESEfinder, RescueESE, NCBI GeneBank, and Swiss-Prot. FASTSNP also uses UCSC Golden Path and NCBI Blast for quality control of candidate SNPs. It also accesses the haplotype database HapMap to obtain information about the haplotype and linkage disequilibrium around a SNP. A table that lists the names, URLs and the usage of these external Web servers is available in the document.
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Where
to get my SNP prioritization results?
FASTSNP allows you to obtain your SNP prioritization results by two ways, email or viewing task on-line immediately. You could enter your email address during prioritization for retrieving results. You may also view the result immediately after you confirm your SNP prioritization task. A link to view your task can display the task you just request, but closing the browser will let you lose that link.
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Why
there is no result for my SNP?
FASTSNP connects to many remote biological Web servers to extract required information to perform SNP prioritization. Those Web servers may be temporarily unavailable at the moment you submit the query to FASTSNP. In that case, there will not be any result returned from those Web servers and FASTSNP will not return the result to you, neither. You might want to try to visit those biological Web servers to see if they are alive and retry the query to FASTSNP later. If the problem persists, please inform us at fastsnp@ngc.sinica.edu.tw.
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Why
it takes so long to complete my request?
FASTSNP connects to many remote biological Web servers to extract required information to perform SNP prioritization. In case when some of the remote Web servers are temporarily unavailable, FASTSNP will wait and retry several times before it gives up connecting to those severs and thus may spend a long time to finish your request. In that case, you might want to cancel the request and try again later. If the problem persists, please inform us at fastsnp@ngc.sinica.edu.tw.