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Table 1 Comparison of SpliceCenter features with those of other web-based splicing resources

From: SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

SpliceCenter Capability

AceView

ASAP

ATSD

fastdb2

Hollywood

EUSplice

ECgene

Splicy

General

        

   Simple, Intuitive Interface

     

  

   Help and Sample Queries

*

*

*

*

Splice Variants

        

   Graphical display of gene's splice variants

   Identifies coding regions

 

  

  

   Identifies NMD targets

   

    

   Human, Mouse, and Rat

*

*

*

*

PCR

        

   Primer sequence query showing position in variants

   

  

 

   Batch high-throughput primer query

        

siRNA

        

   siRNA sequence query showing position in variants

        

   Batch high-throughput hit/miss report for siRNAs

        

Microarray

        

   Display pre-computed target positions of Affymetrix, Agilent, Illumina, and ExonHit probesets in gene's variants

       

*

   Display integrated graphic of microarray probe targets and primer target positions.

        

   Batch high-throughput query of pre-computed probe/probeset target positions

       

*

Peptide

        

   Peptide sequence query displaying source coding region in splice variants

        

   Batch high-throughput peptide query

        
  1. This table shows the capabilities of SpliceCenter in the first column and identifies other splicing database websites with similar features. The comparison is done from the point of view of a biologist interested in investigating the impact of alternative splicing on a sequence-based assay. Other sites contain features not found in SpliceCenter but which are not directly applicable to the focused tasks addressed by our tools. A '✔'indicates presence of a feature, a blank cell indicates absence of a feature, and a '*' indicates partial implementation of a feature.