The gene set for Chicken was built using a modified version of the standard Ensembl genebuild pipeline. Gene models are based on genewise alignments of chicken proteins as well as genetically distant proteins from other species. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The protein based gene models were then extended using Chicken cDNA and EST alignments, the cDNAs were added to models made from chicken proteins and the ESTs to models based on proteins from other species. The resulting gene models were then assessed by generating sets of potential orthologs to genes from other vertebrate species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.