CrowsNest:: A Comparative Map Viewer
CrowsNest CrowsNest

Instructions


Introduction

    CrowsNest is a Comparative Map Viewer at PGSB that uses a dynamic graphical interface to visualize and investigate genome-wide chromsome organization as well as genome-wide synteny between two or more plant genomes. The Map Viewer consists of four different levels of detail for the user to be able to investigate in a top-down manner starting at the macro level. With the increasing number of sequenced and partially sequenced plant genomes there is a growing need for genome comparison in order to elucidate the functions of genes and to study the evolutionary history.

CrowsNest example pf level 2
CrowsNest comparative example view of Level 2 between Oryza sativa and Sorghum bicolor.

How to start using CrowsNest

    There are several easy ways for navigating through the comparative genomic landscape. You can either enter the top level macro view via a specific genome project (this genome is called the target genome throughout the Map Viewer session).
Otherwise you can search for a specific genetic element (location) within a PGSB plant project, e.g. Sorghum bicolor, browse through the details page to the bottom and enter CrowsNest at the mirco level.



Navigating through the different level of details

    You start usually with the crow's nest view which is called the representation level 1. This view visualizes whole genome vs whole genome comparison information either in detail or in a condensed manner. From here you choose a chromosome by clicking on it. The Map Viewer visualizes the complete chromosome vs whole genome comparison information. This is called the representation level 2. The syntenic relationships represented with lines can be clicked on to be referred to level 3. You can navigate to a region of choice to investgate a synteny. If you zoomed into a region smaller than 3 Mbps a click on a syntenic relationship leads you to the graphical representation level 4. In this level you can zoom in close to the nucleotide level and investigate different genomic features, such as tandem repeats, transposable elements, etc. . In order to go back to another level you can use the top navigation bar.



Overview of the four different graphical representation levels
Overview of the four different graphical representation levels



    There are three different navigation panels to use for intuitive navigation. The navigation panel at the top lets you change the representation level and the side bar navigation panel lets you change general viewer features, specific features to a genome, or even the genomes, chromosomes itself. The bottom navigation panel is for browsing the syntenic region of interest.



Navigation panels of CrowsNest
The three different navigation panel of CrowsNest: a) shows the top panel at the top of the Map Viewer,b) at the left hand side and c) at the bottom just below the map image. All panels are created dynamically according to the user request and viewer level.


    The most important graphical features of CrowsNest are the following:
    1) Use the top naviagtion bar to switch to another representation level. If the Map Viewer does not have enough information to display information at the choosen level it evaluates the candidates with the most syntenic relationships. Example: The Map Viewer currently displays level 1. The user chooses the level 3 to be displayed next via the top naviagtion bar. Level 3 requires chromosomes to be set of both genomes, which are not in level 1. The Map Viewer evaluates synteny, chooses both chromosomes and displays the synteny.
    2) The lock aspect ratio feature makes navigation easy as each requested action is performed on all chromosome, such as zoom in, zoom out, up, down, etc. .
    In level 3 and 4 the syntenic relationship which was clicked on is centered according to the region of interest if possible. This feature makes navigation easier there is less need to navigate up, down, left and right.
    3) Genetic features in level 4 are linked to the PGSB plantdb to retreive further information.
A quick guide to CrowsNest graphical features

    The implementation of the CrowsNest Map Viewer was designed to provide a intuitive map-based interactive web interface. The viewer displays macro as well as micro syntenic information at different levels. The top representation level displays syntenic regions as tracks to the right side of the target chromosome. There are as many tracks as the number of reference chromosomes. The tracks are color coded according to the legend at the bottom. You can chose between the detailed and the 'condensed' view.

Example of the top representation level between Sorghum bicolor and Oryza sativa
Example of the top representation level between Sorghum bicolor and Oryza sativa


    The 2nd macro level of CrowsNest displays syntenic information in regard to a specific target chromosome. Only chromsomes with more syntenic relationships than a genome specific cutoff are displyed here.

Example of the level 2 representation of Sorghum bicolor chromosome 5 and synteny to Oryza sativa chromosomes.
Example of the level 2 representation of Sorghum bicolor chromosome 5 and synteny to Oryza sativa chromosomes.


    The 3rd level focus initially on synteny between two chromosomes, one target chromosome of interest and one reference chromosome to the right side. Another chromosome can be added to the left side. Within this level you can zoom in an explore synteny of a region of a minimum of 3Mbps. From there you get into the forth level by further clicking onto a syntenic relationship.

Example of the level 3 visualization of synteny between Sorghum bicolor chromosome 5 and Oryza sativa chromosome 11.
Example of the level 3 visualization of synteny between Sorghum bicolor chromosome 5 and Oryza sativa chromosome 11.


    The 4th level of CrowsNest displays synteny of a region of less than 0.5 MB. There is an synteny overview at the top of the graphical area for easy navigation. Either the syntenic relationships or the chromosomeal regions are clickable to navigate the bottom detailed feature visualization. But there is also the possiblity to click on the syntenic relationships in the bottom area in order to center the complete bottom view.

Example of the level 4 visualization of synteny between Sorghum bicolor chromosome 2 and Oryza sativa chromosome 9.
Example of the level 4 visualization of synteny between Sorghum bicolor chromosome 2 and Oryza sativa chromosome 9.

Data types and genomes compared

    The current version of CrowsNest (10/05/2009) contains syntenic information between two genomes based on physical genome space. However, the Map Viewer was designed to display a variaty of different data, ranging from genetic maps, genomic sequences to BAC/BES based information such as FPC maps.
The table below present synteny that can be explored with the CrowsNest Map Viewer. Any of the 2 genomes can be selected as 'target' and the viewer suggests genomes as 'reference' for which data is available.

Table
Genomes of which synteny was calculated against.

Technical Overview

    The PGSB Comparative Map Viewer provides a web-based front-end to comparative genome datasets in PGSB PlantDB. It is implemented primarily in Perl and makes use of the existing overlaying PlantDB software framework at MIPS. The Perl CGI scripts in the presentation layer make use of HTML::Template and a set of template files. Similarly, URLs (including those of the Perl CGI scripts themselves) are stored in a separate set of XML files and are referenced via an alias. This ensures that each distinct URL appears only once in a centralized location, greatly simplifying maintenance. Additional modules specific to PGSB handle generating the graphical displays and web caching.

Questions and/or Comments?

    Nussbaumer, T. .

CrowsNest was originally developed by Stephan Rössner, a former member of the plant group.
The service is now maintained by Thomas Nussbaumer.