PubMed Nucleotide Protein Genome Structure Taxonomy

Canis familiaris genome data and search tips Revised 8 September 2005

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Canis familiaris, and the search tips specific to that organism. Upon familiarization, return to the Canis familiaris genome overview page or stop by the Map Viewer home page, where you can search the genome data of any organism represented in Map Viewer.

Scope of Data back to top

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

Dog Genomic Sequence Data:
whole genome shotgun (WGS) data		 back to top

The current dog genome build is based on the CanFam2.0 assembly produced by the Broad Institute. The genome was derived from a female boxer. The sequencing strategy produced a 7.6-fold whole-genome shotgun (WGS) assembly.

The mitochondrial genome presented in build 2.1, NC_002008, is not derived from the boxer used for the WGS data but was obtained from a dog of the Sapsaree breed.

BLAST of Dog Genomic Sequence back to top

The complete set of dog sequence databases available for BLAST searching are shown on the dog BLAST page, which includes a link to the database descriptions.

Additional Dog Genome Resources back to top

In addition to the Canis familiaris data available in the Map Viewer and through BLAST, links to NCBI resources and external sites are available from the Dog Genome Resource Guide.

Available Maps back to top

The available maps for Canis familiaris include:

Sequence Maps back to top

Ab initio

Models generated by Gnomon . mRNA alignments were used to segment the genomic sequence by putative gene boundaries, and Gnomon was executed on these segments to predict genes. 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 built using alignments are blue, the models with frameshifts or premature stops are green, and the pure ab initio predictions are brown.

Component

The component map provides the tiling path of GenBank "AAEX01xxxxxxxx" accessions used to build the "NW_xxxxxx" WGS contigs.
Contig

Shows the chromosomal placement of NW_xxxxxx contigs on the assembly of whole genome shotgun (WGS) data.
CpG Island Shows regions of high G + C content on the assembled genome sequence. Two sets of criteria were used for finding CpG islands: "strict" and "relaxed," described below. The algorithm (and cutoffs) were taken from Takai and Jones, 2002.
  • relaxed (shown with light blue shading on the map)
    • 200 bp min length
    • 50% or higher G + C content
    • 0.60 or higher observed CpG / expected CpG
    • post-processing:  merge islands that are <= 100 bp apart
  • strict (shown with dark blue shading on the map)
    • 500 bp min length
    • 50% or higher GC content
    • 0.60 or higher observed CpG / expected CpG
Cfa_RNA Alignment of individual dog transcripts to the assembled genomic sequence.

Hs_RNA Alignment of individual human transcripts to the assembled genomic sequence.

GenBank_DNA

Shows the placement of dog genomic DNA sequences from GenBank on the assembly of whole genome shotgun (WGS) data. Placement is based on the alignment of the sequences to the components (AAEXxxxxxxxx) of the contigs. It includes dog genomic sequences longer than 500 bp that have at least 97% identity to the components for at least 98 base pairs; this includes poodle WGS sequences with accession numbers AACNxxxxxxxxx. If a sequence extends beyond a contig, that portion of sequence is not shown. The 'hits' link leads to a tabular display that shows the matching regions (base spans) of the assembly component and the GenBank genomic DNA record that has been aligned to it.

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 Breed from which the Genbank record was derived, when available.

Genes_Sequence

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.

If multiple models exist for a single gene, corresponding to splicing variants, the Gene_Sequence 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 Transcript (RNA) 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_Sequence 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...)

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 type of evidence that was used to construct the models. The one or two letter code shown in the evidence column (that is displayed when Gene_Sequence is the master map) also indicates the type of evidence.

 
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 RNA

Diagrams of the RNAs that are predicted on the genomic contigs. The RNA map and Gene_Sequence map are built in the same way, using the same types of evidence, described above. The Gene_Sequence map, however, shows a view of all the exons in a gene, while the RNA map shows the combinations of exons (i.e., splice variants) that are valid, based on mRNA sequences.

Repeats Position of repetitive elements

The May, 2002 version of RepeatMasker was executed using these flags:

  • -w flag --invoking MaskerAid
  • -no_is
  • -cutoff 255
  • -frag 20000


STS Placement of STSs from a variety of sources onto the assembled genomic sequence (the NW_xxxxxx contigs, described above) using Electronic-PCR (e-PCR).
Cfa_UniG Alignment of dog EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns 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 Cfa_UniG map and clusters in the UniGene resource.)
Hs_UniG Alignment of human EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns 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 Hs_UniGene map and clusters in the UniGene resource.)
Radiation Hybrid Map back to top

This comprehensive radiation hybrid (RH) map was constructed at the University of Rennes, France using the RHDF5000-2 whole-genome radiation hybrid panel and computed using the MULTIMAP and TSP/CONCORDE programs. The 3270 markers map to 3021 unique positions and define an average inter-marker distance corresponding to 1 Megabase (Mb).

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:

  • symbols
    A search for symbol PNLIP will retrieve the locus named pancreatic lipase. Sometimes two or more symbols refer to the same locus and are considered synonyms or aliases. In this case, either term will retrieve the same information for viewing.
  • GenBank accessions
    e.g., a search for accession AB113380 will retrieve the map representing the chromosome to which this sequence aligns.
  • markers
    e.g., a search for USP11 will retrieve the chromosome X map containing this STS marker. If a marker alias exists (i.e., L03387), either one of the terms will retrieve the marker.
  • text terms
    e.g., 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 Entrez 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 on the left 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

Allowable Values back to top

For Canis familiaris, the following types of map positions can be entered in the left sidebar text boxes noted in option 1:

  • symbols - you can enter gene symbols, marker names, or alternate symbols or marker names 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 - can be used if the master map is a genetic map, radiation hybrid map, YAC map, or sequence map. It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (centiMorgans, centiRays, ordinal units, or bases, respectively).

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 Entrez 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. 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 outlined 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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