Aluru Lab | Ashlock Lab | Schnable Lab

• Blast
  • MAGI
  • SAMI
  • Repeats
  • Assembled ESTs
  • 454 ESTs
  • Sequenced BACs
  • UA & CAU 5' ESTs
  • Mapped markers
• Annotation
  • View a MAGI
  • View an EST
  • NIPs (GBrowse)
  • Repeatmasker
• Genetic Mapping
  • View maps (CMap)
  • Browse/Search Data
    • ISU-IBM markers
    • ISU-IBM Mapped
      Sequences
    • ISU-SNP Markers
  • Mapping Requests
    • Submit Request
    • View Status
• Download
  • Assemblies
  • Repeat DB
  • Gene Predictions
  • ISU mapped Seq
• Info
  • MAGI / SAMI
  • Methods
  • Assembly Statistics
  • Publications
• People
• Sponsors
• What's new
• FAQs
• Sign up for Updates

Overview

Welcome to the MAGI website, which summarizes some of our investigations of the maize genome. These analyses have been facilitated by our NSF-funded IBM BlueGene/L supercomputer. We have assembled gene-enriched (MF and HC; Whitelaw et al., 2003; Palmer et al., 2003) and random Whole Genome Shotgun (WGS) GSSs (Genome Survey Sequences) of maize and sorghum into MAGIs (Maize Assembled Genomic Islands) and SAMIs (Sorghum Assembled genoMic Islands), respectively. Based on computational and biological quality assessments it appears that a very high percentage of genic MAGIs and SAMIs accurately reflect the structures of the maize (Fu et al., 2005) and sorghum genomes. We have similarly assembled maize ESTs into MECs (maize expressed contigs). It is possible to Blast MAGIs, 454-ESTs, MECs, SAMIs and the 16,819 B73 maize BACs that as of 10/09/2009 have been at least partially sequenced by the maize genome sequencing project ( DBI-0527192; Rick Wilson, PI). MAGIs have been annotated via sequence similarity, repeats, alignments to Sanger and 454 ESTs, and using an ab-initio gene prediction tool. A repeatmasker is available to facilitate primer design and annotation. Our latest genetic map, ISU_IBM Map7, contains ~6,000 genic markers integrated with ~4,000 additional markers from other projects. This map has been fully integrated into the MAGI web site. It is possible to blast sequences against the ~6,000 sequence-defined, genic, genetic markers generated by the ISU maize mapping project. If you find the MAGI web site useful we request that you mention it in your talks, posters and publications. The appropriate citation for the MAGI dB is Fu et al., 2005. If you'd like to use the MAGI logo on a poster or slide you can get it here. This material is based upon work supported by the National Science Foundation under Grant DBI# 0321711 and CNS-0130861. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.