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

OLego: Senstive and fast splice mapping for mRNA-seq reads.

SpliceTrap: Exon inclusion ratio estimation from paired end RNAseq data.

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)