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

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.

ISSN: 1471-2105