Schematic representation of the flow of data through the SSHscreen-SSHdb pipeline. SSH was used for the construction of a cowpea drought expression library. Tester cDNA were prepared from drought stressed IT96D-602 cowpea leaf RNA and driver cDNA from control Tvu7778 cowpea leaf RNA, and vice versa for the reverse library. The subtracted library was spotted onto glass slides and hybridised with a mix of differently labelled subtracted and unsubtracted cDNA from the two cowpea cultivars. The R package SSHscreen 2.0.1 was used to analyse the microarray data, using limma functions for pre-processing the data as well as to identify statistically significant differentially expressed genes. A subset of clones was selected for sequencing. Available FASTA sequences as well as top tables (output from SSHscreen) were uploaded to the web-based database, SSHdb, to manage and annotate clones in the library. Expression results for selected genes were verified using qPCR.