PubMed Nucleotide Protein Genome Structure Taxonomy

Neurospora crassa genome data and search tips Revised June 7, 2004

The Map Viewer Help document describes how to use the Map Viewer software. This page describes the data available for Neurospora crassa and the search tips specific to that organism. You can also return to the Neurospora crassa genome view search page. The Map Viewer homepage allows you to search the genome data of any organism represented in Map Viewer.

  1. Scope of Data
  2. Available Maps
  3. Types of Mapped Objects and Maps on Which They Can Be Found
  4. Constructing Queries
  5. Constructing URLs

Scope of Data back to top

The Map Viewer provides a graphical view of the Neurospora crassa genome (assembly version 3) sequenced, assembled, and submitted by Whitehead Institute Center for Genome Research. After the automated annotation was performed and released to the public, the Whitehead Institute initiated a Community Analysis Project to study the Neurospora crassa genome in close collaboration with more than 30 members of the Neurospora research community. This collaboration resulted in the publication of: Galagan JE et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003 Apr 24; 422(6934):859 - 868.
 

Available Maps back to top

The available maps for Neurospora crassa include:

Map Name Description
Sequence Maps back to top

Contigs The contig sequence map shows the genomic chromosome assembled from the components. Only 67 contigs (of total 173 constituting N.carssa genomic sequence) have been anchored to the genetic map by locating the position of genetic markers within the current assembly using BLASTN. Only a subset of the well-ordered markers has associated sequence, and thus only these few markers (a total of 279) have been used to order and orient contigs against the genetic map. The contig sequence map has an accession in the format NW_XXXXXX.

Component The Component (Comp) map provides the tiling path of RefSeq accessions (in a format AABX_XXXXXXXX) used to build each of the contigs of the chromosome sequence map. Of total 821 components, 511 have been positioned on the map.

Gene Genes that have been annotated on the chromosome sequence map.

mRNA mRNA corresponding to each gene that has been annotated on the chromosome sequence map.

Genetic Linkage Maps back to top

Genetic

The genetic map consists of approximately 1000 genetic markers placed within seven linkage groups (chromosomes). The original genetic maps show the ordered positions of some of the markers within the linkage groups.

Constructing queries back to top

Searchable Terms back to top

Text terms back to top

The Neurospora crassa data are searchable with the following types of terms:
  • gene symbol (e.g. rifin)
  • gene name (e.g. NCU03574)
  • marker name (e.g. Met-6)
  • Contig and components accession number (e.g. NW_047161)
  • RefSeq mRNA accession number (e.g. XM_322731)

Truncation back to top

Search terms can also be truncated or include wild cards, as explained in the truncation section of the general Map Viewer Help document. For example, the following searches will retrieve the merozoite surface protein (MSP1) gene:

  • MSP1
  • MSP?   (each question mark represents a single character; multiple question marks can be used)
  • MSP*   (an asterisk represents zero to many characters)

Map Positions back to top

As noted in the Search by Position section of the Entrez Map Viewer general help document, there are three main ways to search by map position from the Map View of a chromosome:

  1. Enter a range of interest in the Region text boxes in the sidebar.
  2. Click on the region of interest in the chromosome thumbnail graphic in the sidebar.
  3. Click on a region of interest in the enlarged Map View of the chromosome.

For Neurospora crassa the following types of map positions can be entered in option 1:

  • marker names - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system for the range search to work. For example, if the Genetic Map is the Master Map, then you can enter the microsatellite marker names to get the range of display based on the marker names.
  • gene symbols
  • numerical positions - in basepairs.

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 bottom of the chromosome. If you enter the value only in the lower box, the Map Viewer will display the region of the chromosome starting at the top of the chromosome and ending at the value you entered.

Constructing URLs that link to Map Viewer back to top

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region.

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