A description of the various features available upon installation of AceBrowser-MODS-3.1.2.tar.gz .

View the objects of a selected class
   The AceBrowser search script now has the capability to view database objects on a per class basis. Go to the
    GrainGenes  page and click on a class name in the box at the bottom of the page. A scrolling list will appear containing a
    sublist of object names, each representing the first entry on each page. Clicking a sublist element brings the page into view.
    Use the Search Pattern textbox to further refine the scrolling sublist.

Use the JalView sequence alignment  viewer.
    Look at graphic display of this sequence and then click the "View Alignment" link. The page which appears displays 3 buttons
    marked: CAP3, PHRAP and ClustalW. Clicking any of these will cause the selected alignment program to run
    and a JalView applet button to appear after the alignment calculation is complete. Clicking this applet button then
    activates the JalView sequence alignment viewer where the homologies can be viewed.

Hyperlink AceDB objects to external databases .
    Allows AceDB objects to be linked to external URLs, this feature was previously found only in
    the WebAce browser and I have borrowed much of the related code from that fine software.
    Here's a sample. Observe the the EMBL,TIGR and wEST hyperlinks next to the External_DB field. Compare
    with this view  from the original AceBrowser-3.1 tree script.

    A patch for the LongText display problem has also been encorporated in this implementation. The patch, supplied
    by Keith Bradnam @ UK CropNet, allows objects of type longText to be displayed w/proper HTML formatting.
    Observe it here!.

Mousover display of Locus information.
   This modification enables the "pic" script to show descriptive information on mouseover. Heres an example. Place the
    mouse pointer over the locus Xbcd508-1D (green highlight) . In the status bar of your browser will appear Homology
    and E-value information for this locus.

An implementation of an Ace Query Language (AQL) web interface.
    Ace Query Language: it's no longer just for the command line!  AqlInterface enables the use of AQL in a
    web-browser. Special thanks to Matthew Couchman of UKCropnet whose code for TableMaker and
    AQL_Builder provided much insight for my implementation.

View a sequence and its homologies in fasta format/ auto-paste into BLAST form.
    Select a particular sequence. Click the "View as Fasta" link at the top of the page to display the
    sequence of interest and its homologies in fasta format. Click the "Blast" link on the tool bar to automatically
    copy/paste the sequence into a BLAST form.

View a Keyset in fasta format.
    Allows the user to view a set of sequences as fasta formatted text. Observe both of the following examples. The
    first one uses the "search" script  while the next uses the "query"script. Clicking the "View in FASTA Format" link
    allows the current page of 100 sequences to be viewed in fasta format. The user might then copy/paste any of the
    displayed sequences into another software application for further processing.

    Back to the download and configuration page.

Acknowledgments:
The scripts and modifications described in this document were by no means created in a vacuum.
Without the previous work by numerous people on such diverse tools and software as: Acebrowser, WebAce,
AceDB, Perl, AcePerl, CGI.pm, Emacs, Apache, Linux and this NSF grant, none of this work would have been possible.

If you have Any questions or experience installation problems: email me!
Hugh Edwards Aug_14_02