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Found 1 entry:Ensembl ContigView
See also extra information on ContigView displays for species other than human:
Introduction
Features in 'Detailed View' panel
DNA (contigs)
IntroductionEnsembl 'ContigView' is the principal data visualisation tool for genome sequence annotation information. It provides a high level view of the contig sequences that form the human genome sequence assembly, and of genes and other features that have been placed on it. 'ContigView' can be customized to suit you. More information can be added, or the displays can be simplified to make browsing faster. Please look at the options for customizing the display. The page is split into four sections representing different levels of zooming into the chromosome:
The red boxes on the assembly in the 'Chromosome', 'Overview' and 'Detailed View' panels represent the regions shown at higher magnification in the panel following below. The absolute base pair location of the region displayed in 'Detailed View' is indicated in the navigator bar at the top of 'Detailed View'. You can use this bar to navigate along any chromosome by entering a new chromosome and/or location (you can specify kb/k or Mb/M as well as entering numbers in base pairs). The search box at the top of the page allows you to search for any identifier present in Ensembl (see Ensembl Search). ChromosomeThe 'Chromosome' panel displays an ideogram of an entire chromosome with its cytogenetic banding pattern. Maps of cytogenetic bands to the genome seqeunce allow just for crude orientation and are not available for all species. For all those species with genome sequence assemblies in a pre-chromosome stage, Ensembl displays other 'top-level' sequence entities such as 'scaffolds'.
The red box illustrates the extent of the region displayed in the
'Overview' panel below and can be moved by clicking anywhere on the chromosome.
The 'Chromosome' display can be turned on or off using the
OverviewThe 'Overview' panel displays a larger section of a chromosome together with its basic annotation. Usually the range is set to 1 Mb but can be smaller for species with genomes of higher density. The 'Overview' panel displays the following information:
The red box illustrates the extent of the region displayed in the subsequent
'Detailed View' panel below.
You may click anywhere in the
'Overview' panel to re-centre the red box at that point on the contig map.
The 'Detailed View' display below will change accordingly.
Except for re-centring contigs and genes are not clickable in the
'Overview' display, but they are selectable in the
'Detailed View' panel below.
The 'Overview' display can be turned on or off using the
Navigation Bar
Clicking on one of these buttons will move the whole display 1 or 2 Mb to the left or right. The size of region represented by the red box will not change.
Clicking on one of these two buttons will scroll the whole display to the left or right by 80% of the current display length. The size of the red box will not change.
By default, 'Detailed View' shows a region of 1000 kb. These buttons above provide the option to zoom in and out, varying the size of the region displayed. Use this to restrict or expand the field of view to a scale suitable to view any feature of interest. Click on steps in the ramp to display 1, 5, 10, 50, 100, 200, 500 kb or 1 Mb. Clicking plus or minus zooms in or out by a factor of approximately 2, and allows zooming in to as little as 1 bp. Regions larger than 1 Mb can only be seen in the 'Overview' panel. Generally, 'CytoView' is recommended for viewing larger segments of a chromosome.
To move to a different chromosome or to specify a chromosomal location in base pairs, enter numbers in the appropriate boxes and click on
To specify a display between two markers, use
'MapView'.
You can also navigate by mouse-over on the scale bars at the top and bottom of the 'Detailed View' panel. This brings up a clickable menu that lets you zoom or re-centre the 'Detailed View' display. Detailed ViewThe third panel 'Detailed View' shows small regions of chromosomes and provides more detailed information on genome sequence annotation. Features shown for the human genome are described here. There are some differences for other species - see also the additional information for mouse, rat, zebrafish, pufferfish, mosquito, fuit fly, Caenorhabditis elegans, Caenorhabditis briggsae.
The 'Detailed View' display panel can be turned on or off using the
The DNA sequence is again represented as alternating dark and light blue contigs. The colour-coded features above the contigs are positioned on the forward strand and those below are on the reverse strand of the genome seqeunce in standard notation. Feature tracks are named at the left side of the 'Detailed View' panel. Blue names indicate tracks served from external DAS sources via the Distributed Annotation System. Tracks may be turned on or off and customized to suit your requirements. Pointing to a feature with the mouse ("mouse-over") will bring up text showing the feature's name and links to more detailed information where available. These pop-up menus can be turned off by unchecking "show pop-up menus" in the "Decorations" pull-down menu. A single click on most features will take you to an appropriate page with more information on that feature (unless you have chosen to display pop-ups by clicking on a feature only). (See customizing the display for more details.)
DNA (contigs)The 'DNA (contigs)' track shows a representation of the genomic sequence assembly. How the assembly was prepared, and how it is represented in Ensembl 'ContigView', differs in different Ensembl species. See information on how the display differs in mouse, rat, zebrafish, pufferfish, mosquito, fuit fly, Caenorhabditis elegans, Caenorhabditis briggsae. The human assembly is based on the sequence of individual BAC clones. A finished BAC clone will consist of a single contig sequence. Alternating dark and light blue blocks show individual contigs that make up the chromosomal assembly. Hovering the mouse cursor over the contig bar will bring up the full designation of the contig and the accession number of the clone from which it is derived. There is also a clickable link to the appropriate EMBL sequence file. Clicking on a contig centres the display on that contig. The arrowheads show the orientation of the contig sequence given in the EMBL source file relative to the chromosome assembly. Where no blue contig is shown, there is a gap in the assembly. For more information about gaps in the assembly, see the gap track. Transcripts'Detailed View' does not display genes as such but rather their transcripts. Transcripts shown above the blue 'DNA (contigs)' bar are transcribed in the forward direction (left to right), while transcripts shown below the bar are transcribed in the reverse direction (right to left). Ensembl considers genes as a collection of exons - from which there may be many transcripts. Each exon is represented by a coloured box, and the exons in a transcript are joined by angled lines. Untranslated regions of the transcript (5' and 3' UTRs) are now shown as coloured outlines, while the predicted coding regions are shown in solid colour. This distinction is seen best when viewing relatively small regions of a chromosome. If there are several transcripts at the same point on the sequence then that gene has been assessed as producing multiple transcripts (displayed on different lines). ENSEMBL TRANSCRIPTS track shows the Ensembl predicted transcripts. "Known transcripts", which correspond closely to near-full-length species-specific cDNA and/or protein sequences already available in the public sequence databases, are shown in red. "Novel transcripts", which cannot be matched with confidence to specific database entries are shown in black. Note that all the Ensembl predictions (known and novel) are strongly supported by similarity to protein or cDNA sequences. Mouse-over a "known" or "novel" Ensembl transcript will produce a menu with the Ensembl transcript id (ENSTXXXXX) or assigned name at the top, followed by additional identifiers and links:
Clicking on a transcript takes you directly to 'GeneView'.
VEGA TRANSCRIPTS
More information about the preparation of these gene sets can be found on the human chromosome 20 and chromosome 22 pages at the Sanger Institute, at Genoscope for chromosome 14 and Washington University for chromosome 7. Mouse-over a blue curated transcript will produce text showing the name/identifier and the category of gene, and clickable links to 'GeneView', 'TransView' and 'ProteinView' pages. You can also reach the 'GeneView' page by a single click on the transcript. EST TRANSCRIPTS displays transcript predictions made by Ensembl using EST evidence alone. You may wish to compare these predictions with those in the main transcripts track. Clicking on an EST transcript takes you to a modified 'GeneView' page, which summarises the transcript structure, outlines the prediction method, and shows the sequence of the predicted transcript. Pointing to an EST transcript brings up a menu with the identifiers (e.g. ENSestTxxxxxx) and links to 'GeneView', 'TransView' and 'ProteinView' pages. GENSCAN tracks show transcripts predicted ab initio by the GENSCAN gene prediction programme. GENSCAN is run on individual contigs, so predictions do not span more than one contig. Pointing to a transcript shows a non-stable identifier based on the contig and the start and end of the Genscan prediction in the contig, plus links to 'FASTAView' pages with the sequence of the predicted transcript and protein. Information about these predictions can also be accessed by exporting a flat file of the region, with 'prediction features' selected. See ExportView for more details. You can also download a complete set of GENSCAN-predicted transcripts or peptides. SNAP tracks display transcripts predicted ab initio by the Semi-HMM-based Nucleic Acid Parser (SNAP). Like GENSCAN, it predicts transcripts solely on the basis of the underlying genomic sequence and does not take any experimental evidence into account. The SNAP track is not available for all species, but SNAP performs better than GENSCAN in some species. Displays of gene and transcript predictions from NCBI and other groups may be available as DAS sources. Protein homology evidence
Evidence for Ensembl gene predictions, taken from protein sequence entries in databases.
The presence of an entry in an evidence track shows that it has significant homology with at least one of the exons displayed in an Ensembl or Genscan transcript.
The data sets displayed differ for the different Ensembl species. See information on how the display differs in:
PROTEINS
mRNA Homology Evidence
Evidence for Ensembl gene predictions, taken from mRNA sequence entries in databases.
The presence of an entry in an evidence track shows that it has significant homology with at least one of the exons displayed in an Ensembl or Genscan transcript (except for the ESTs track and the human cDNA track which show all above-threshold hits to the assembly - see below).
The data sets that were used for the gene predictions and that are displayed in
'ContigView' differ for the different Ensembl species.
See information on how the display differs in:
UniGene
EMBL mRNAs
Human cDNAs
ESTs
(not shown by default)
tRNA
(not shown by default)
Eponine
(not shown by default)
First Exon Finder
(not shown by default)
Start/Stop
(not shown by default)
The following features are strand independent and are shown at the bottom of the 'Detailed View' panel. Only 'Markers', 'QTLs' 'SNPs' and 'Haplotypes' have clickable links. Whole Genome Similarity Matches(not shown by default - turn on using the Compara menu on the golden bar) This table summarizes the species involved in whole genome comparisons, as well as the programs used for the analysis and the abbreviations used for the track label. Conserved Regions ('cons bz' track) and Highly Conserved Regions ('high cons bz' track) Untranslated whole genome comparisons are performed for species pairs which are thought to be similar enough to be able to detect homology at the DNA level. BLASTzis used to compare the species pairs as shown in the table. Most of the BLASTz data were obtained from UCSC.After they run BLASTz the alignments are cleaned and grouped into 'chains' using the AxtChain algorithm. See the UCSC website for complete details of the parameters used for each of the species pairs. Occassionally Ensembl and UCSC are out of sync with the assemblies, or have not performed a comparison that is of interest to the Ensembl user. In these cases we run BLASTz comparisons in house and arrange the alignments into simple groups based on synteny. This procedure is under developement at the moment. These then are the 'cons bz' tracks. The 'highly cons bz' tracks are produced in house by rescoring the blastz alignments (either from UCSC or those produced in house) with a much stricter 'TIGHT' nucleotide scoring matrix For those (using the 'subsetAxt' program from Jim Kent, UCSC) with a gap open penalty of 2000 and a gap extension penalty of 50. The minimum score threshold was 3400. A C G T A 100 -200 -100 -200 C -200 100 -200 -100 G -100 -200 100 -200 T -200 -100 -200 100
These tracks ('high cons' and 'cons') may be toggled between grouped and ungrouped displays by clicking the red
Translated BLAT ('trans BLAT' track) The translated BLAT is used to compare genomes from more evolutionarily distant species, at the amino acid level. Thus regions of similarity will be biased towards those that code for proteins, although highly conserved non-coding regions might be detected as well. The softmasked database sequence is translated in all 6 reading frames and is stored in memory as an index of no overlapping 5 amino acid mers. These 5-mers are then compared to the query sequence, also translated in all 6 reading frames, to find regions of likely similarity, which are then extended into full ungapped alignments. The scoring matrix is a simple +2/-1 matrix, which also helps to speed up the querying. N. B. All similarity matches are strand independent tracks and are therefore displayed at the top of the 'Detailed View'. For more information about regions of conserved synteny, look at 'SyntenyView'. MarkersMouse-over will show the id of the marker and the option to view the details and synonyms in 'MarkerView'. Note that only a sub-set ot the markers stored in the Ensembl databases are displayed - information about other markers may be found via an Ensembl search. QTLs(Quantitative trait loci) Only a preliminary mapping of rat QTLs is available at present. See rat ContigView help. CpG Islands
(not shown by default)
SNPs
(not shown by default)
Indels (insertions and deletions) are marked with an arrowhead. When zoomed in on a small region (in the Base Pair view panel, for example) you can see the ambiguity code for the SNP polymorphism. Mouse-over on any SNP will produce a menu with the SNP id at the top and additional information. Depending on the source of the SNP data various links are available. A direct click will take you to 'SNPView'. SNP properties will take you to 'SNPView', providing a summary of data about this SNP. HGBASE data, TSC-CSHL data and dbSNP data will take you directly to entries in these SNP databases. SNP information (alleles and ambiguity code) shown in 'SNPView'is taken from the dbSNP entry. To see the alleles and effects as appropriate to a transcript or protein, look at the SNP information in 'TransView' and 'ProteinView'. Haplotypes
(not shown by default)
Repeats
(not shown by default)
Tile Path and other displays of clones and contigs
Different information is shown for the different Ensembl species.
See information on how the display differs in:
The tile path track in human Ensembl shows the sequence entries (mostly BAC clones) that were used in the current assembly, and where they map on the assembly. Clones for which FISH-mapping information is available are marked with a blue corner. Where a clone is shown in outline (open bar), the mapping of the clone to the sequence assembly is problematic and the true length is not displayed. The different colours (red and orange) are used only to help distinguish one clone from another. Mouse-over brings up information about the clone. You may want to jump to 'CytoView' to access more information about clones. The VEGA clones track in human Ensembl shows clones that have been manually annotated and appear in the VEGA database. Gaps
(not shown by default)
%GC
(not shown by default)
DAS sourcesSee additional information on mouse DAS displays.
DAS (Distributed Annotation System) provides a way of making extra annotation visible.
The DAS sources in the DAS pull-down menu are made available via the
Sanger Institute.
Tick to select sources.
The selected tracks will be displayed when you close the menu.
The names of DAS tracks are shown in blue in the
'ContigView' panel.
Different DAS sources will be available by default in different Ensembl species. See additional information on mouse displays. Pointing to features in most DAS tracks will produce a pop-up menu showing an identifier, and one or more links to view the associated sequence in FASTA format in an Ensembl 'FastaView' page. The 'FastaView' page also provides, where possible, a brief description of the data source and a link to a web page from the group that provided the data for the DAS track. The sources shown by default in the human DAS menu may include:
Basepair ViewThe fourth panel is used to show features on a small segment of the assembly. By default, 'Basepair View', shows a region of 100 bp, taken from the centre of the 'Detailed View' panel. The display can be zoomed in or out, and moved left or right, using navigation controls similar to those of the 'Detailed View' panel. These buttons above provide the option to zoom in and out, varying the size of the region displayed. Use this to restrict or expand the field of view to a scale suitable to view the sequence of interest. Click on steps in the ramp to display 25, 50, 100, 200, 300 and 500 bp. Clicking plus or minus zooms in or out by a factor of approximately 2, and allows zooming in to as little as 1 bp. Regions larger than 500 bp can only be seen in the 'Detailed View' panel.
The 'Basepair View' panel can be turned on or off using the
SequenceThe sequence of the genomic assembly (forward strand above the DNA(contigs) bar, reverse strand below). It can be turned on or off via the 'Decorations' pull-down menu. Each of the 4 bases has a different background colour, to make it easier to visualise runs of bases. The actual bases are shown when there is room in the display. Amino acidsTranslations of the assembly sequence. All three possible reading frames are shown, above the DNA(contigs) bar for the forward strand, below it for the reverse strand. The tracks are turned on or of via the 'Decorations' pull-down menu but will only display information when you are viewing 500 bp or less. Each amino acid has a different background colour, and amino acids with related properties have related shades:
The IUPAC single letter codes for the amino acids are shown when there is room in the display. Restriction EnzymesShows sites that could be recognised and cut by restriction endonucleases. The sequence of the site is shown in colour (blue for enzymes that cut the 2 DNA strands in a staggered fashion to produce 'sticky ends'; green for enzymes that cut the 2 DNA strands at the same point to produce 'blunt ends'), together with the name of the enzyme. Red vertical lines mark the expected cut positions (joined to the recognition site where necessary by horizontal lines). Pointing to a site produces a pop-up window with the name of the enzyme and its general recognition sequence. Customizing the displayWe provide a variety of ways for you to customize the 'ContigView' displays. Some features are not displayed by default, but can be added. Turning off unwanted features and functions will make the web pages download faster and make it easier to see the features of interest to you. Customizing is done using:
'Chromosome',
'Overview',
'Detailed View' and
'Basepair View'
can each be turned on or off using the
The pop-up menus that appear when you point to a feature with the mouse can be turned off by unchecking the 'show popup menus' option on the 'Decorations' pull-down menu on the gold bar. This may speed your browsing (at the cost of some useful functionality). You can still click on a feature to go to a default information page. An alternative way of using the pop-ups is now available: you can choose to have pop-up menus appear only when you click on a feature (check the '... popup on click' option on the 'Decorations' menu). However, if you plan to use Ensembl regularly it is well worth getting used to the default behaviour of the pop-up menus (see hints).
Features, Repeats, Decorations and DAS sources
The overall image size is set by default to a width of 700 pixels. This is appropriate for standard-sized screens. The 'Image size' pull-down menu on the gold bar allows you to adjust the width up to 1500 pixels. ExportThis pull-down menu on the golden bar gives several options for downloading the data represented in the 'Detailed View' panel. 'Flat file', 'FASTA' and 'Image' will redirect you to an 'ExportView' page preset to the extent of chromosome displayed in 'Detailed View' and to the kind of download you have requested. Ensembl gene list, EST gene list, Vega gene list and SNP list will redirect you to the EnsMart data mining system, with the displayed region and choice of focus already selected. Jump to ...Options on this pull-down menu (located on the golden bar) allow you to jump to the same region displayed in Ensembl 'CytoView', view direct comparisions to other species in Ensembl 'MultiContigView', or to jump to Ensembl 'MapView'. You can also view the same region displayed in the Human Genome Browser at UCSC, or in Map Viewer at NCBI. HelpAn additional pull down menu on the golden bar gives you the option to jump directly to help on the configuration page, a convenient way of customizing 'Detailed View', more information on 'DAS Sources' this general help page for 'ContigView' and to a page for sending questions or comments to the Helpdesk. Mouse-over and "tooltip text"For most features in the 'Detailed View'panel, you can display extra information and links by pointing with the mouse. Putting the mouse pointer over a feature ("mouse-over") brings up a pop-up text window ("tooltip text"). The text looks like a menu. The top menu item is a name or database identifier (bold text and not clickable). Below this may be one or more information points (text in grey and not clickable), and one or more clickable links (text in colour). So that the display does not become cluttered, the pop-up text windows stay on the screen for only about 6 seconds. Click on the X at top-right to close immediately. (The window will also disappear if you move the pointer onto a different feature.) To re-display, move the pointer off the feature and then point again. To click on a displayed link, move the mouse pointer down the menu - the hand link symbol will appear when you are over a clickable link.
Hints:
Does the pop-up window disappear when you try to move the pointer onto it?
You have probably moved through another feature without realising it.
Try moving slowly onto a feature and stop moving when the text appears.
If you keep having problems, zoom in on the region you are exploring, so that features are not so close together.
You can also click directly on most fe |
Date : 2004-10-27 13:18:32 | ![]() |
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