Zhang Lab: Computational Biology and Bioinformatics

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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.

• LSPD: The Liver Specific Gene Promoter Database

• SCPD: Yeast Promoter Database (public)

• VertPD: Vertebrate Promoter Database (Internal to CSHL staff only)

Software Tools

• HMDFinder: Methylation prediction in human genome.

• DME (Internal only)

• DME, SCPD, MARSMotif and MARSMotif-M stand alone version is available from the authors
see Software Licensing

• 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-SPC at 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: CorePromoter (public), CoreBoost (public) and
CoreBoost_HM (public)

• Human poly(A)-site prediction (public)

• Human promoter mapping using CpG islands (public)

• MatCompare

• Multisequence alignment (Internal to CSHL staff only)

• FTP resources

• CIPHER (public)

Software Licensing (DME, MARSMotif, MARSMotif-M, SCPD, TRED)