Table 1

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

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

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.

Ryan et al. BMC Bioinformatics 2008 9:313   doi:10.1186/1471-2105-9-313