SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays

20 pages, 13 figures.-- Supplementary material available at: http://genomebiology.com/2008/9/2/R46/additional/ (Additional data file 1: 22 Figures. Additional data file 2: Matlab data files).-- PMCID: PMC2374713.Exon and exon+junction microarrays are promising tools for studying alternative splicing. Current analytical tools applied to these arrays lack two relevant features: the ability to predict unknown spliced forms and the ability to quantify the concentration of known and unknown isoforms. SPACE is an algorithm that has been developed to (1) estimate the number of different transcripts expressed under several conditions, (2) predict the precursor mRNA splicing structure and (3) quantify the transcript concentrations including unknown forms. The results presented here show its robustness and accuracy for real and simulated data.This project was partially funded through the 'UTE project CIMA' and an FMMA grant to LMM. APM was partially funded by Spanish grants PR27/05-13964-BSCH, CAM-P2006/Gen-0166, TIN2005-05619 and by Spanish Ramón y Cajal program.Peer reviewe