Table 3.

Global comparison of available salmon databases

	SalmonDB	GRASP	ASALBASE	Gene index
Data
Data source	All public ESTs	Public ESTs, BAC ends	BAC clones, BAC ends and EST cluster	NCBI ESTs
Base pair quality	No	Yes	No	No
EST assembly	CAP3, clustering	Phrap	No	Clustering, CAP3
Physical map	No	No	Yes	No
Genetic map	No	No	Yes	No
Expression data	No	Yes	No	No
Tools
Blast homology search	Yes	Yes	No	Yes
Quick search box	Yes	No	Yes	No
Primer design	Yes	No	No	No
RepeatMasking	No	Yes	No	No
GO annotation browser	Yes	No	No	Yes
KEGG annotation browser	Yes	No	No	Yes
Advanced search with Biomart	Yes	No	No	No
Analysis
Ortholog prediction	Yes	Yes	Yes	No
Paralog prediction	Yes	No	No	No
SNP prediction	Yes	No	No	Yes
CDS prediction	Yes	Yes	No	Yes
Other markers	No	No	Yes	No
Full-length cDNA prediction	Yes	Yes	Yes	No
Alternative splicing forms prediction	No	No	No	Yes
Others
Web interface	Gbrowse	Gbrowse	Gbrowse, custom	custom
Other organism data	5 fish species	Other salmonids and salmon lice	4 fish species and Human	Other TIGR organisms

cGRASP information was extracted directly from the http://web.uvic.ca/grasp/ website that includes features from external links. Gene index information was obtained from the website http://compbio.dfci.harvard.edu/tgi/.