PubMed Nucleotide Protein Genome Structure Taxonomy

Nasonia vitripennis genome data and search tips Revised August 1, 2007

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Nasonia vitripennis (parasitoid jewel wasp) and the search tips specific to that organism. You can also return to the Nasonia vitripennis genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in Map Viewer.

  1. Scope of Data
  2. Available Maps
  3. Constructing Queries
  4. Constructing URLs

Scope of Data back to top

The Map Viewer provides a view of jewel wasp data from a variety of sources described below.

Jewel Wasp Genomic Sequence Data back to top

The current jewel wasp genome build (1.1) is based on the Nvit_1.0 assembly of May 2007 (AAZX00000000) provided by the Human Genome Sequencing Center at Baylor College of Medicine. The genome was sequenced using a whole genome shotgun (WGS) approach, with BAC and fosmid end sequences used for scaffolding. 263 scaffolds and singletons suspected of being bacterial or vector contamination were removed from the Nvit_1.0 assembly during the NCBI annotation process. None of the contigs have been placed on chromosomes.

BLAST of Jewel Wasp Genomic Sequence back to top

The complete set of jewel wasp sequence databases available for BLAST searching is shown in the pop-up menu on the jewel wasp BLAST page, which includes a link to the database descriptions.

Additional Jewel Wasp Genome Resources back to top

In addition to the jewel wasp data available in the Map Viewer and through BLAST, links to NCBI resources and external sites are available from the Jewel Wasp Genome Resources Guide.

Available Maps back to top

The available maps for jewel wasp include:

Sequence Maps back to top

Ab initio

Shows gene prediction models generated by Gnomon. Gnomon uses protein alignments in addition to transcript alignments and, in order to capture as much coding information in the genome as possible in this assembly, Gnomon models may represent partial as well as complete coding sequences. Models with a completely supported CDS are blue, models with a partially supported CDS are green, and the pure ab initio predictions are brown. Those ab initio predictions with e values <0.0001 are indicated as dark brown on the map and all other ab initio predictions are shown in light brown. Pure ab initio status indicates that the model was built without the support of mRNA or protein alignments, either through failure to align the sequence to the genome or an alignment ignored by Gnomon due to a score falling below a pre-determined threshold.

For jewel wasp Gnomon predictions, transcripts from both Nasonia vitripennis and Nasonia giraulti were treated equally. A collection of EST sequences generated by C. Desjardins, D. Oliveira, R. Edwards, P. Dang, D. Lee, J. Colbourne, H. Tettelin, W. Hunter, and J. Werren were provided prior to publication to provide additional model support.

Component

Provides the tiling path of GenBank accessions used to build each of the "NW_xxxxxxxxx" contigs, described below.

Contig

Shows the chromosomal placement of NW_xxxxxxxxx contigs on the assembled genomic sequence. The individual GenBank records used to assemble the contigs are shown on the Component map, described above.

Nvi RNA Shows the alignment of individual Nasonia vitripennis RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Nvi UniG map, described below.

Ngi RNA Shows the alignment of individual Nasonia giraulti RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Ngi UniG map, described below.

Ame RNA Shows the alignment of individual Apis mellifera (honey bee) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Ame UniG map, described below.

Ins RNA Shows the alignment of individual Insecta (true insects) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Ins UniG map, described below.

GenBank DNA

Shows the alignment of Nasonia vitripennis genomic DNA sequences from GenBank that were not used in the assembly of contigs. It includes jewel wasp genomic sequences longer than 500 bp that have at least 97% identity to the components for at least 98 base pairs. If a sequence extends beyond a contig, that portion of sequence is not shown. 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 were aligned. When the GenBank DNA map is displayed as the master map, in the default verbose mode, the descriptive text includes several columns: 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 were 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.
Gene

Genes that have been annotated on the genomic contigs. This includes known and putative genes placed as a result of alignments of mRNAs to the contigs, and gene predictions.

If multiple models exist for a single gene, corresponding to splicing variants, the Gene map presents a flattened view of all the exons that can be spliced together in various ways. For example, if one splice variant uses exons 1, 3, 4, and another splice variant uses exons 2, 3, 4, the Gene_Sequence map shows exons 1, 2, 3, 4. (In comparison, the RefSeq Transcripts map shows what combinations of exons are valid based on mRNA sequences from RefSeq and GenBank.)

Genes shown on the left of the grey line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down).

When Gene is selected as the Master map, the verbose display (detailed labeling, shown by default) includes arrows to the right of each gene name indicate its direction of transcription as well as links to:

  • sv - sequence viewer (more...)
  • pr - protein (more...)
  • dl - view/download sequence data from a chromosome region (more...)
  • ev - evidence viewer (more...)
  • mm - Model Maker (more...)

Additional information about these links is also provided in the Entrez Map Viewer Help Document, under Links to Related Resources.

Gene models are shown in five colors, depending on the quality of the alignment of defining RNA RefSeqs to reference genome, and the maintenance of the coding sequence based on the placement.

 
Gene Color Evidence Code Type of evidence used to construct gene model
Blue C Confirmed gene model - model based on alignment of mRNA, or mRNAs plus ESTs, to the genomic sequence (see additional notes, below)
Light Green E EST only - model based on EST evidence only
Dark Brown PE Predicted+EST - model predicted by Gnomon and EST evidence (more about Gnomon)
Light Brown P Predicted only - model predicted by Gnomon (more about Gnomon)
Orange ? Conflict - there is some discrepancy between the mRNA sequence and the gene model (see additional notes, below)
  I Interim LocusID - model based alignment of mRNAs, or mRNAs plus ESTs, to the genome, in which the aligning transcripts could not be unambiguously assigned to a preexisting LocusID (see additional notes, below)

  Additional Notes:

In general, a gene model is shown in blue if there is a clean alignment between a RefSeq or GenBank mRNA sequence and the genomic sequence, and if there is an exact match between the protein product that was annotated in the mRNA sequence record and the conceptual translation of the genomic sequence gene model.

A gene model is shown in orange if there is some discrepancy between the mRNA sequence and the gene model, either in the alignment of the two and/or in their protein products. Examples of the former can include gaps, or the alignment of an mRNA to two or more genomic regions. Examples of the latter can include differences between the amino acid sequence given in an mRNA sequence record and the conceptual translation of the corresponding gene model, or premature termination of a coding region in the genomic sequence. Both of those can be caused by base pair mismatches between the mRNA and genomic sequence.

Models with Interim LocusIDs (evidence code I) may be paralogs, genes not yet curated, duplications because of assembly errors, or pseudogenes. The genome assembly and annotation pipeline assigns interim IDs when there is no unambiguous solution to what they should be. Interim LocusIDs are always associated with a RefSeq XM_* accessions (model mRNAs), although supporting alignments may (or may not) include RefSeq NM_* accessions (known mRNAs). More about RefSeq and RefSeq accessions can be found at the RefSeq homepage.

RefSeq Transcripts

Diagrams of the RNAs that are predicted on the genomic contigs. The RefSeq Transcript map and Gene map are built in the same way using the same types of evidence. The Gene map, however, shows a view of all the exons in a gene while the RefSeq Transcript map shows the combinations of exons (i.e., splice variants) that are valid if mRNA sequences indicate alternative splice variants.

Repeats Position of repetitive elements. RepeatMasker was used to illustrate areas within the genome that contain low complexity DNA sequences.

Nvi UniG Alignment of Nasonia vitripennis 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. Those 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 Nvi UniG map and clusters in the UniGene resource.)

Ngi UniG Alignment of Nasonia giraulti 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. Those 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 Ngi UniG map and clusters in the UniGene resource.)

Ame UniG Alignment of Apis mellifera (honey bee) 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. Those 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 Ame UniG map and clusters in the UniGene resource.)

Ins UniG Alignment of Insecta (true insects) 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. Those 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 Ins UniG map and clusters in the UniGene resource.)
Constructing queries back to top

Searchable Terms back to top

The Map Viewer supports searching on any term that describes an element on any map, including:

  • gene symbol
    A search for Eve will retrieve the locus even-skipped.
  • marker name and alias
  • GenBank accession number
  • text words
    For example, a search for actin 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 back to top

As noted in the Search By Position section of the Map Viewer 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 side bar
  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 Nasonia vitripennis, the following types of map positions can be entered in option 1:
  • symbols - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work properly.

  • numerical positions - It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (i.e. bases for sequence maps). Note that for a sequence map, base pair positions may be entered in any of the following formats: 1000000 or 1,000,000 or 1M or 1000K.

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 back to top

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), field restriction, or 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, although this option currently is not applicable for searching Nasonia vitripennis since none of the contigs have been mapped to chromosomes. The Advanced Search page is accessible from the header region of the genome view page.

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. For example:

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