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 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) and CoreBoost (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 (DME, MARSMotif, MARSMotif-M, SCPD, TRED)