Steps Programs  or algorithms Roles Websites 1 Repeats Identification Censor Finds repeats and masks homologous portions. http://www.girinst.org/censor/index.php TREP and BLASTn Discovery and annotation of repetitive elements. http://wheat.pw.usda.gov/ggpages/Repeats/blastrepeats3.html DNA Subway Repeat sequences masking and gene predictions. http://dnasubway.iplantcollaborative.org/ 2 Gene Identification and functional annotations FGENESH Polish annotations http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind. DNA Subway and Augustus Gene Prediction, Annotation of Genomic Sequences. http://dnasubway.iplantcollaborative.org/ andStanke et al. [48]. BLASTn Finds ESTs that match proteins. blast.ncbi.nlm.nih.gov BLASTp Finds possible proteins. TREP and BLASTp Predicts proteins. http://wheat.pw.usda.gov/ggpages/Repeats/blastrepeats3.html 3 Primer designs Primer 3. Primer design http://www.simgene.com/Primer3 and Rozen and Skaletsky [24]. Programs used to annotate the putative soybean rust resistance gene Rpp3 tightly linked to marker Satt460. Some programs were multi-purpose i.e DNA subway and BLAST algorithms used for identification of repeat and putative genes. BLASTn find ESTs (expressed sequence tags)

Table 2: The algorithms used to analyse Rpp3 gene in Soybean (Glycine max) query sequence from DNA base 43291218 – 44292393 in the NCBI database and their roles.