Written originally for the C. elegans sequencing project, the software is used to manage genetical and physical map data and DNA sequences from a variety of plants, animals and prokaryotes. The bulk of the sofware has been written by Jean Thierry-Mieg(mieg) and RichardDurbin(rd). Queries about the code can be addressed directly to firstname.lastname@example.org, email@example.com, or firstname.lastname@example.org.
Compiled versions of the software together with documentation for users and links to other sites can be found at this site, along with a list of viewable databases.
Inside ACEDB, context-sensitive Help pages can be accessed from every window. These pages are also available online. A news group exists at bionet.software and is a good source of help.
ACEDB was originally written for the Xwindows interface of UNIX machines. THE UNIX VERSION IS DESCRIBED HERE but versions for Windows and Macintosh are also available.
Opening an AceDB Database
Your system administrator will usually set up a script allowing you to type "acedb" on the command line.
The First View of AceDB :
The first X window to open is the CLASS window. This MAIN or CLASS window lists the most frequently used classes of object modelled in your database. It has a Title giving the name of the database and version number and the version of software in use. It has buttons with drop-down menus, also, facilities for calling for a list of stored objects and performing word searches on the database.The data models for each class of object modelled in the database can be viewed from here. There is a unique background menu associated with this window in that it provides the only way of quitting the database.
The second window appears after a double Left Mouse (LM) click on an Class. It is called the KEYSET window and this gives a list of the objects requested from the class window. This window also has a background menu as well as several button function boxes at the top of the window. From this window it is possible to select an object to view.
Selecting and Viewing Objects in AceDB :
The original UNIX-based version of ACEDB was written for use with a 3- button mouse. The left-mouse (LM) button is used for selecting an object, the right-mouse(RM) button for pulling down a menu and selecting an item from it, the middle mouse (MM) is used on graphical map displays for zooming in or out, or re-centring the display on a new object. Selecting an object with LM can be done EITHER by a double click, or, by highlighting its name first, then giving another click to fetch it. Every object is displayed in its default display.
The Main Types of Display
- Class and Keyset windows
- Tree or text window
- Genetic Map (Gmap)
- Physical map (Pmap)
- Feature or Sequence display (Fmap)
- Peptide display (Pepmap)
- Blixem alignment tool
- Metabolic pathways
- Data dumping and data input
- Dendrogram (Phylogeny tree)
- KEYWORD SEARCHES
- GENERAL SEARCHES
- QUERY LANGUAGE
- TABLE MAKER
- KEYSET MANIPULATIONS
- DNA ANALYSIS
- GENE FINDING
- [Quit] to close the window,
- [Biblio] to pull out associated papers if available
- [Attach] to include data kept in another object.
- Show as text overrides default display for graphical objects
- Biblio fetches and displays citations *
- Neighbours fetches related objects
- Export data fetchs file dump
- Toggle timestamps
- Expand a list of objects
- Contract a list of objects
- marker genes
- a long black chromosome bar
- genetic rearrangements
- a physical map contig bar in yellow
- a scale,
- genetic marker loci.
- a locator bar showing the position(green box) on the sequence (black bar)
- a white bar showing the main and any overlapping sequences
- a yellow bar showing the active part of the display (non-active is blue)
- a scale in DNA bases.
- show multiple DNA alignment
- show multiple DNA alignment of just this kind of homologies
- Develop a table of these homologies
- Export Sequence
- Export Translation
- Export Features
- Quit : gets rid of this window
- Print : prints the current window
- Clear : clears all the boxes, giving clean slate
- New Keyset : puts the answer in new window thus allowing you to keep the previous answer
- By example : brings up the Query by Examples window
- Command Edit : brings up the plain (but powerful) query facility window,
- Search Locally : does the search
- Undo (see under Query below)
Other Tools Provided
Each database is set up differently but, generally, objects which can be displayed graphically will be called first in their graphical form from which you can call the text version of the object. DNA sequences show up directly on the Fmap, genes on the Gmap, clones on the Pmap, filters etc on the Grid, proteins on the Pepmap, metabolites and pathways on the metabolism display.
Most other objects will appear in the text or TREE window.
Navigation Around and Between Windows
Text or tree windows have buttons which respond to single LM click:
All windows have a background RM drop-down menu, with a sliding select function. Each menu includes :
Preserve enables the user to open more than 1 text window simultaneously. Normally, the same window is overwritten by each newly called object.
Help calls context sensitive help for that window in HTML format.
Calling up a text-based object such as Person or Paper will demonstrate the basic navigation pattern and the structure of the database.
The Class name and Object name are given at the top of the window. Inside the text is shown in a tree layout. The root is at the top left hand corner and comprises the unique object name or identifier. The main branches are TAG names for the data fields, or leaves, which follow the tags. Tags can be subdivided into sub-tags or secondary tags, tertiary tags and so on.
Data fields can be of normal types such as free Text, integers and real numbers, dates, or pointers to other objects in the database.The latter are shown in bold text in tree displays. A LM click on one of these bold items brings up a new window. In the Paper object below, the article title is free Text, the Pages are integers, Journal and Author are pointers. The Locus tag is followed by an arrow and number. A LM click will expand this into a list of Loci. A second click will contract it.A double LM click on one of the authors will open that object in a new window. From that author, one can navigate to another Paper and so on.
The Abstract Tag in Paper is special. It points to a piece of LongText, which is handled differently by the software. This can be also be called independently from the Paper containing it.
In addition, text window menus include these options.
* this is database dependent
I THE GeneticMAP
The textual information for every object shown on the map can be fetched by a double LM click. The desired object is also highlighted in blue and its database name and brief details are shown in the long blue bar a the top. The Gmap is built up from a series of columns. The nature and order of these varies with database. Column definitions can be viewed by a LM click on the green bar at the bottom. Some databases give a selection of map views, seen with a RM click on the Views button. LM brings up the column control panel, allowing the user to alter the display and redraw it for just that user session. It is customary for clones and genetic rearrangements to be shown as vertical lines or boxes and genes shown as point objects.
In this example there are from leftwards :
Positioning the LM on the green slider bar moves the view up or down the map, whereas the MM pulled rightwards from the bar magnifies and leftwards telescopes the view. The zoom buttons at the top do this in steps.
The Gmap data button has two modes, LM automatically displays the map data stored for an object which has already been highlighted, RM brings down a specialist menu for curators.
The RM menu from the Highlight button can be used in conjunction with a Keyset of items which are listed in the Keyset window.For instance, you could highlight all displayed items starting with letter "S".
Each linear and each point object has a RM menu used by curators for moving objects but the point object also has the option to display Likelihood distribution, which shows how good the map position is for that object.
Any objects related by positive or negative mapping data to the selected object may be shown in other colours: here green represents genes included within a rearrangement, blue marks those outside, dark green and dark blue depict those objects with conflicting data.
In this C. elegans map, a LM click on the yellow Contig bar will take the user to the same place on the Pmap, a horizontally orientated physical map of cosmids and YACs. In other databases, users may be taken to sub-Maps, or to Sequence displays (Fmap).
II THE FMAP
This is the most complex display. It was designed for showing DNA sequences and for analysing and annotating them. Like the Gmap, the Fmap is based on a series of columns which may differ in usage and position between databases. Common features will be demonstrated from a C. elegans example. Many menu options are intended for curators and not mentioned further.
From the left, users can see :
The following colour code is database dependent, those below are used for C.elegans :
mid-blue = BlastX homologies to Swissprot
yellow = EST homologies to C. elegans
red = EST homologies to other worms
green = tandem and inverted repeats
dark red = Tc1 insertion sites
dark blue = C.briggsae homology
purple = C.briggsae homology
cyan = Prosite motifs.
Finally there are brief comments together with the names of the subsequences, names of matching ESTs, corresponding genes (if any).
Moving around the Fmap can be done the same way as the Gmap. The zoom buttons and mouse zooming and moving are the same. Clicking on any object (LM) will give its name in the blue bar at the top and fetch the text display for that object. It will also be highlighted in pink. To view genes on the upstrand, click LM on Rev_Comp button.
To alter the display, click with RM on columns button to get a drop down menu, or LM to get the menu at the bottom. Clicking on items will toggle them on/off in the display.
DNA can be displayed by LM on the DNA button, a second click removes DNA. Exons, splice sites and stop sites can be coloured by choosing highlight exons on the RM menu on an exon. Highlighted motifs are marked on the yellow bar.
To analyse the DNA, LM on Analysis button will give a new window, in which you can submit a restriction site or other motif. These sites will be displayed on the DNA in cyan (green for complement) and on the yellow bar.
Translations can be turned on either by using the RM on an exon or by using the Columns button for all 3-frames. LM on Columns button gives a choice of boxes, one per column. Grey is on, white is off. RM on columns give a very long slide-down menu. Simply click on and off the words in the list (no visible change on list). The Fmap is re-drawn.
Using the Genefinder button (LM) will produce a three frame display of potential ATG (small yellow boxes) and stop codons (black lines), Genefinder exon predictions (grey boxes), HeXon predictions for coding sequence (orange boxes) and a rightmost column of splice sites, the longer the better. For boxes, the broader the better.
LM on an DNA (EST) homology will produce the Blixem menu :
A double LM click on a protein homology will produce a Pepmap image if the peptide sequence is stored in the database or the text window for the object.
Even non-curators can export data from a read only database. RM on the background reveals a choices of formats to dump :
The exons RM menu also permits dumping of the tranlsation and the cDNA. The features file comes as a Table in gene-finding format.
III THE PEPMAP
This is very similar to the Gmap display with columns defined at the bottom, zoom buttons and the top blue bar for object identification. The peptide sequence can be coloured by LM click on the Peptide section at the bottom, then follow the bu ttons on the new window, remembering to toggle on the radio button. Next to the sequence is a hydrophobicity plot and rightwards are depicted protein homologies. The Analysis button (RM) calls a Dotter window with a dot-plot of the peptide against itself.
(Blast multiple alignment display).
This was written by Eric Sonnhammer. The top part shows the length of and percentage homology of the other proteins or DNA sequences for the target and below this, the portion contained in the sliding box is and shows a list of these proteins and their sequence by coding frame. Identical residues are dark, similar residues are light blue. Picking one of the MSPs above will highlight it in cyan thus showing where it crossmatches in other parts of the target sequence.
The Grid map is mainly used in genome databases to display hybridisation results. In the C. elegans database, a representation of a 96-well grid of YACs is used to store hybridisation patterns of cDNAs and other YACS for mapping purposes. The Grid can be reached by asking for the Grid Class on the main window. Also, the Grid can be shown by following the Positive_probe Tag inside Clone objects. The RM menu provides Toggle functions for showing the YAC names, or the content of wells can be seen in the top Gridded_item box by one LM click. Typing the word clone, followed by a YAC or cDNA name at the top of the window, next to Probe: will highlight the grid cells which give strong (dark) and weak (light) blue hybridisation signals.
VI METAB DISPLAY
After getting a list of Pathway objects, you can select any pathway and see the display. A double LM click on an arrow, a pathway step box, a metabolite or a co-enzyme will bring up the text information. Enzymes can only be reached from within the text window of a pathway step.
VII DENDROGRAM DISPLAY
This display can be used to represent many types of data : protein or DNA molecular similarity trees, species taxonomy, worm cell lineages and any other heirarchical data. These displays can be called under the Tree class on the main window.Subtrees may be collapsed/expanded by single LM clicks. A double LM on a node calls associated data, such as cells from the worm lineage.
Query and Table Making Facilities
Using version 4.6 software : on the class or main window, get the pull down menu with RM and select in turn Query by Examples, Query builder, Query, Table Maker. Using version 4.7 software : use RM on the Query box to get drop-down menu, or LM to get free-standing menu for queries.
This is the simplest way to query the database and the least powerful. You can do a query on one class at a time by selecting the class from the box preceeded by Class:. Use LM or RM to get a list of classes, slide down and release to select one.
For example, to get Authors with E_mail addresses and published papers : select Class Author then highlight the TAGs E_mail and Paper then click LM on the Search box.
This query facility is rather unstable but useful for beginners.
Some simple examples are :
(1) Allele ITEM NAME begins with e* END (2) Locus Phenotype contains lethal END (3) Paper Author COUNT is greater than 2 END A more complex example is : (4) Allele ITEM NAME begins with e and Sequence exists ENDTo activate a query, either press return on the END box or click on the Search Locally box.
To use this you need to have a fairly good knowledge of the database and its data structures or at least of the class you want to search. It is advantageous to have open a window with the data model of your class. There is a help menu for the query syntax.
- quit : gets rid of this window
- print : prints the current window
- clear : clears all the lines, giving a clean slate
- new keyset : puts the answer in another new window, allowing you to keep the previous one
- By Example : brings up the Query by Examples window
- Builder : brings up the Query Builder window
- Load : loads in a pre-formatted query from the wquery directory
- Save : saves a query in the wquery directory (the query syntax not the answer)
- Search : searches the active keyset, or the whole database
- Undo : allows one to travel back one step up a list of queries to a previous anwer or keyset
Some simple queries could be : >?Sequence Transcript tRNA >?Author (Sequence OR Paper) >?Locus (Positive_clone & Phenotype = *pharynx*) if you follow the Locus query with this on the next line : >COUNT Allele > 1 You get a subset of the previous loci. Using undo will give you back the Loci which have been cloned and which alter pharynx.
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