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Project Documentation & Protocols: Maize Gene Discovery Project: Genomic Survey Sequences

ZmDB collects all the maize genomic survey sequences (GSS) from GenBank regularly. Users can download the sequences from ZmDB download center. More general information about GSS can be found at NCBI dbGSS. The following are organizations contributing maize genomic DNA sequences:

Automatic annotation of the GSSs at ZmDB is currently done by searching GenPept using the NCBI Blastx program. Only hits with an E value smaller than 1e-10 are selected, corresponding to proteins with high degree of sequence similarity to the DNA sequence inferred translation products. Automatic annotation is aided by the program MuSeqBox (Multi-query SEQuence Blast Outout eXamination), developed in our group. For each query sequence, the top hits (if any) are selected and annotated as potential homologs of the inferred DNA sequence. Keywords of these hits are also used as the keywords of the DNA sequence. This allows the ZmDB users to search the database by keyword for sequence of interest using either Text Search or ACE Query. Table Maker can be used to extract such information for all or a large batch of the ZmDB sequeces. A link to the record of each hit at NCBI is provided. In addition, GeneSeqer, also developed in our group, is used to match maize ESTs to all the GSSs. The sequence alignment and a diagram are presented for each GSS.

The above chart summarizes the growth in GSSs over the past few years.

This chart shows the division of contributions among those who have provided GSSs.

Dr. Bedell, Orion Genomics
Dr. Bennetzen, Purdue University
Dr. Martienssen, Cold Spring Harbor Laboratory
Dr. McCombie, Cold Spring Harbor Laboratory
Dr. Morgante, Dupont Genomics
Dr. Okagaki, University of Minnesota
Dr. Pauls, University of Guelph
Dr. Schnable, Iowa State University
Dr. Settles, University of Florida
Dr. Schroeder, University of Missouri
Dr. Walbot, Stanford University
Dr. Whitelaw, TIGR
Dr. Wing, Clemson University

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