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MaizeGDB becomes 'sequence-centric'.

Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ - Database (Oxford) (2009)

Bottom Line: Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes.Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation.In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.

ABSTRACT
MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org.Database URL:http://www.maizegdb.org.

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The result page for the approximate genomic coordinates for the opaque endosperm1 (o1) locus when the Locus Lookup tool is used.
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Figure 3: The result page for the approximate genomic coordinates for the opaque endosperm1 (o1) locus when the Locus Lookup tool is used.

Mentions: Maize is a species with a long genetic history, and over 1700 genetic maps are currently available via MaizeGDB. Because genomic coordinates are not available for all loci and some genetically mapped loci are not cloned, a mechanism for estimating the genomic location of such loci is needed for, e.g. researchers walking to genes. To meet this need, the Locus Lookup Tool (Figure 3) was implemented. The Locus Lookup Tool (available from the MaizeGDB front page, the Genome Browser and throughout MaizeGDB in other relevant locations) works by first checking physical map coordinates to find out whether the locus is already placed. If so, the physically mapped locus is highlighted in red in the appropriate genomic region. If not, the tool checks the locus record at MaizeGDB to find out if any sequenced BACs are known to detect the locus, and, if so, that BAC is returned within its genomic context. If not, genetically mapped probes that are nearest to the input locus are identified, the tool checks whether those probes have known genomic coordinates (working outward until appropriate probes are identified) and finally the region of the genome contained by the identified probes is reported with bounding probes shown in red.Figure 3.


MaizeGDB becomes 'sequence-centric'.

Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ - Database (Oxford) (2009)

The result page for the approximate genomic coordinates for the opaque endosperm1 (o1) locus when the Locus Lookup tool is used.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2964019&req=5

Figure 3: The result page for the approximate genomic coordinates for the opaque endosperm1 (o1) locus when the Locus Lookup tool is used.
Mentions: Maize is a species with a long genetic history, and over 1700 genetic maps are currently available via MaizeGDB. Because genomic coordinates are not available for all loci and some genetically mapped loci are not cloned, a mechanism for estimating the genomic location of such loci is needed for, e.g. researchers walking to genes. To meet this need, the Locus Lookup Tool (Figure 3) was implemented. The Locus Lookup Tool (available from the MaizeGDB front page, the Genome Browser and throughout MaizeGDB in other relevant locations) works by first checking physical map coordinates to find out whether the locus is already placed. If so, the physically mapped locus is highlighted in red in the appropriate genomic region. If not, the tool checks the locus record at MaizeGDB to find out if any sequenced BACs are known to detect the locus, and, if so, that BAC is returned within its genomic context. If not, genetically mapped probes that are nearest to the input locus are identified, the tool checks whether those probes have known genomic coordinates (working outward until appropriate probes are identified) and finally the region of the genome contained by the identified probes is reported with bounding probes shown in red.Figure 3.

Bottom Line: Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes.Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation.In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.

ABSTRACT
MaizeGDB is the maize research community's central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17 and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects' data sets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org.Database URL:http://www.maizegdb.org.

Show MeSH