Databases

• AEDB: Alternative Exon Database
• AtProbe: Arabidopsis thaliana promoter binding element database (public)
• CEPDB: C. elegans Promoter Database
• CSEdb: Conserved sequence elements database (public)
• CSHLmpd: Cold Spring Harbor Laboratory Mammalian Promoter Database (public)
• TRED: Transcriptional Regulatory Element Database (public)
• Drosophila Promoter and Gene Expression Database (Coming soon), try one of its components: DBSD: Drosophila Binding Site Database, and another component: CREB target genes Preliminary Results (Internal only)
• LSPD: The Liver Specific Gene Promoter Database
• SCPD: Yeast Promoter Database (public)
• VertPD: Vertebrate Promoter Database (Internal to CSHL staff only)

Software tools

• HMDFinder
• DME (Internal only)
• DME stand alone version is available from the authors
• Comprehensive Regulatory Element Analysis and Detection (CREAD) (open source)
• ESEfinder : Exon Splicing Enhancer Finder
• FirstEF : Human First Exon Finder (public)
• First Exon Prediction
• Gene-finding (public)
• MZEF-SPCat EBI
• AAT at MTU(GSA2=MZEF+ESTs)
• An Example: Using MZEF to Find Internal Coding Exons.
• Genomics of Transcriptional Regulation website
• Human core-promoter prediction(public)
• Human poly(A)-site prediction (public)
• Human promoter mapping using CpG islands (public)
• MatCompare
• Multisequence alignment (Internal to CSHL staff only)
• FTP resources
• Software Licensing