Schizosaccharomyces pombe genome data and search tips

Revised May 21, 2008

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Schizosaccharomyces pombe (fission yeast), and the search tips specific to that organism. You can also return to the Schizosaccharomyces pombe 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 Schizosaccharomyces pombe Genomic Sequence Data BLAST of Schizosaccharomyces pombe Genomic Sequence Additional Schizosaccharomyces pombe Genome Resources Available Maps Genetic Linkage Maps Genetic Sequence-Based Maps Component Contig Genes RefSeq Transcripts Constructing queries Searchable Terms Map Positions General Tips Constructing URLs

Scope of Data

Schizosaccharomyces pombe Genomic Sequence Data

BLAST of Schizosaccharomyces pombe Genomic Sequence

The complete set of Schizosaccharomyces pombe sequence databases available for BLAST searching is shown on the Schizosaccharomyces pombe 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 Schizosaccharomyces pombe Genome Resources

In addition to the Schizosaccharomyces pombe data available in the Map Viewer and through BLAST, Schizosaccharomyces pombe 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 Schizosaccharomyces pombe include:

Genetic Linkage Maps

Genetic

Shows the genetic linkage data that were downloaded from the Sanger Institute's ftp site.

Sequence-Based Maps

Component

Provides the tiling path of GenBank cosmid accessions used to build each of the assembled chromosomes. The cosmid sequences were submitted to GenBank/EMBL/DDBJ by the Sanger Institute.

Contig

Shows the complete/assembled chromosomes. The chromosome sequences, which have RefSeq NC_###### accessions, are curated copies of the assembled chromosome sequences submitted to GenBank/EMBL/DDBJ by the Sanger Institute.

Genes

Shows the gene annotations provided by the Sanger Institute on the assembled chromosome sequence. 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.

RefSeq Transcripts

Shows the mRNAs that have been annotated on the genome assembly. The mRNAs, which have RefSeq mRNA NM_######### accessions, are curated copies of the mRNAs provided by the Sanger 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.

Constructing queries

Searchable Terms

The Schizosaccharomyces pombe data are searchable with the following types of terms: accessions e.g., NM_001019610 or NC_003421 gene symbols/systematic names/locus-tags e.g., a search for the symbol rpl25a will retrieve the locus named 60S ribosomal protein L25. 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., ery1 text words e.g., a search for synthase 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 Schizosaccharomyces pombe, 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