Magnaporthe grisea genome data and search tips

Revised May 23, 2008

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Magnaporthe grisea (rice blast fungus), and the search tips specific to that organism. You can also return to the Magnaporthe grisea genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer. Scope of Data Magnaporthe grisea Genomic Sequence Data BLAST of Magnaporthe grisea Genomic Sequence Additional Magnaporthe grisea Genome Resources Available Maps Genetic Linkage Maps Genetic Sequence-Based Maps Component Contig GenBank DNA Genes Marker RefSeq Transcripts Mgr_RNA Mgr_UniGene Constructing queries Searchable Terms Map Positions General Tips Constructing URLs

Scope of Data

Magnaporthe grisea Genomic Sequence Data

BLAST of Magnaporthe grisea Genomic Sequence

The complete set of Magnaporthe grisea sequence databases available for BLAST searching is shown on the Magnaporthe grisea BLAST page, which includes a link to the database descriptions. In addition, those interested in comparative genomics can use the fungi genomes BLAST page, which allows BLAST searching of sequence databases for a number of other fungi either individually or in combination.

Additional Magnaporthe grisea Genome Resources

In addition to the Magnaporthe grisea data available in the Map Viewer and through BLAST, Magnaporthe grisea genome information can be accessed using the Entrez Genome Project Database. The NCBI Handbook includes a series of exercises that demonstrate additional questions that can be answered with Map Viewer.

Available Maps

The available maps for Magnaporthe grisea include:

Genetic Linkage Maps

Genetic

Shows the genetic map described in Nitta N et al. Theor. Appl. Genet. 95:20-32, 1997. The genetic map data were obtained from the file combined_optical_genetic_maps.xml (dated 12/05/2006), which is available from the Broad Institute's Download Sequence site.

Sequence-Based Maps

Component

Provides the tiling path of RefSeq NZ_AACU02###### accessions used to build each of the NW_######### contigs. The NZ_AACU02###### sequences are curated copies of the WGS contig sequences that were submitted to GenBank/EMBL/DDBJ as part of WGS project AACU00000000.2 by the Broad Institute.

Contig

Shows the chromosomal placement of RefSeq NW_######### contigs on the assembled genomic sequence. The NW_######### sequences are curated copies of the WGS scaffold sequences that were submitted to GenBank/EMBL/DDBJ as part of WGS project AACU00000000.2 by the Broad Institute.

GenBank DNA

Shows the placement of Magnaporthe grisea genomic DNA sequences from GenBank on the assembled genomic sequence. The placement of the GenBank sequences is based on the alignment of these sequences to the contigs. The length of a line represents the upper- and lower-most points on the genome assembly to which sequence fragments from a single GenBank record aligned. Thick parts of a line represent the sequence fragments from a GenBank record that aligned to the assembled genome sequence; thin parts of a line connect the aligned fragments from a single GenBank record. When the GenBank_DNA map is displayed as the master map in the default verbose mode, the descriptive text includes several columns: Hits, which links to a tabular display showing the matching regions (base spans) of the GenBank genomic DNA record and the contig to which it has been aligned; Total Bases, which shows the total number of bases in the GenBank record; Aligned Bases, which shows the total number of bases from that record that aligned to the genome; % identity for the alignment; % coverage, which shows how much of the GenBank record aligned to the genome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the genome to the alignment length of the GenBank record; and Strain from which the GenBank record was derived, when available.

Genes

Shows the genes that have been annotated on the genome assembly by the Broad Institute. Genes shown on the left of the gray line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down). The Genes map presents a flattened view of all the exons in a gene. For example, if two splice variants are predicted for a given gene, and one splice variant uses exons 1, 3, 4 and the other splice variant uses exons 2, 3, 4, the Genes map shows exons 1, 2, 3, 4.

Marker

Shows the placement of markers from the genetic map on the assembled genomic sequence. The marker placements were obtained from the file combined_optical_genetic_maps.xml (dated 12/05/2006), which is available from the Broad Institute's Download Sequence site.

RefSeq Transcripts

Shows the mRNAs that have been predicted on the genome assembly. The mRNAs, which have RefSeq model mRNA XM_###### accessions, are curated copies of the mRNAs annotated on the genome assembly by the Broad Institute. Transcripts shown on the left of the gray line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down). The RefSeq Transcripts map shows combinations of exons that are valid. For example, if two splice variants are predicted for a given gene, and one splice variant uses exons 1, 3, 4 and the other splice variant uses exons 2, 3, 4, the RefSeq Transcripts map shows two transcripts for that gene: one with exons 1, 3, 4 and the other with exons 2, 3, 4.

Mgr_RNA

Shows the alignment of individual Magnaporthe grisea mRNAs and ESTs to the assembled genomic sequence. The mRNAs are indicated by blue lines; the ESTs are indicated by green lines.

Mgr_UniGene

Shows the alignment of Magnaporthe grisea EST clusters to the assembled genomic sequence. ESTs are clustered based on shared exon-intron boundaries and alignment to a common position on the genome. Co-aligning ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Mgr_UniGene map and clusters in the UniGene resource.)

Constructing queries

Searchable Terms

The Magnaporthe grisea data are searchable with the following types of terms: accessions e.g., XM_370222 or U60290 gene symbols/systematic names/locus-tags e.g., a search for the symbol MGG_00604 will retrieve the locus named beta-tubulin. Sometimes two or more symbols refer to the same locus and are therefore considered synonyms or aliases. In these cases, any one of the terms will retrieve the locus. marker names e.g., 1-7-C text words e.g., a search for kinase will retrieve all map objects containing that word in their description. If multiple terms are entered, they will automatically be combined with the 'AND' Boolean operator.

Map Positions

As noted in the Search By Position section of the general Map Viewer Help document, there are three main ways to search by map position from the Map View of a chromosome: Enter a range of interest in the Region text boxes in the left sidebar. Click on the region of interest in the chromosome thumbnail graphic in the sidebar. Click on a region of interest in the enlarged Map View of the chromosome. For Magnaporthe grisea, the following types of terms can be entered as map positions in the left sidebar text boxes noted in option 1: symbols/markers/accessions - you can enter gene symbols/systematic names/locus-tags, markers, or accessions to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on maps that share the same coordinate system as the master map in order for the range search to work properly. numerical positions - can be used if the master map is a sequence map or a genetic map. It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (i.e., basepairs for the sequence maps and centiMorgans for the genetic map). Note that for a sequence map, basepair positions may be entered in any of the following formats: 1000000 or 1,000,000 or 1000K or 1M. It is not necessary to enter a value in both Region text boxes. If you enter a value only in the upper box, the Map Viewer will display the region of the chromosome starting from that point and ending at the lower end of the chromosome. If you enter a value only in the lower box, the Map Viewer will display the region of the chromosome starting at the upper end of the chromosome and ending at the value entered.

General Tips

As mentioned in the Searchable Terms section of the Map Viewer Help Document, any term entered in the query box will be treated as an independent entity to be joined by the 'AND' Boolean operator. It is also possible to construct more complex queries by using explicit Boolean operators (AND, OR, NOT) and field restrictions, and by limiting retrieval to records that have certain properties. The Advanced Search page allows you to use a number of query options by simply checking boxes or radio buttons that represent various search fields, properties, and object types. It also allows you to limit your query to one or more chromosomes. The Advanced Search page is accessible from the header region of the genome view page.

Constructing URLs that link to Map Viewer

Questions or Comments? Write to the NCBI Service Desk