Here we describe the top level menu bar that appears when viewing search results I.e. results from the IP workflow and Blast workflow. Using items in this menu bar you can

• get information on the search.
• launch other applications.
• create reports.
• export sequences in standard formats.

Contents 1 Result Menu 1.1 Saving Virtual Reference Databases 2 View menu 3 Export 3.1 Create reports 3.2 Export sequences 4 Applications 4.1 Pop-up Dialog 4.2 Limits 4.3 List of available applications

Result Menu

1. Result information shows a pop-up with information on the search which created this result like: information about the query, database(s) searched, parameters and strategy used for the search and ownership & sharing status of the result.
2. Save Workspace: saves the current state of the workspace which includes the filters & grouping applied, columns chosen to be displayed and the check box status of various results.
   NOTE: the next time this result is accessed, it will be displayed in this saved state.
3. Reset Workspace: removes a saved workspace so that when the result is accessed next time, it will be displayed in the default state.

Saving Virtual Reference Databases

Note that the result menu when you are browsing sequence databases rather than result databases is different.

The most important operation here is to save the sequences in view as a Virtual database. When browsing multiple sequence databases, you can apply filters to drill down to the particular sequences of interest and then push the Save as Virtual Database item under the Result menu. As an example, it order to create a virtual database of kinase mRNA sequences from human and rat:

1. Go to the Reference Nucleotide Databases list on the My GenomeQuest page, choose RefSeq mRNA, Genbank Primate division and Genbank Rodent division by checking the boxes next to them.
2. Click Browse sequence databases button at the top of the table.
3. When the sequences open, apply filters like the following:
   1. Organism contains Homo sapiens or Rattus norvegicus. The OR between the two terms can be applied by clicking the little + link next to the text box and entering the two terms with a carriage return between them.
   2. Description contains Kinase

With these filters, you now have the kinases from human and rat in your lsit. Now click the Results -> Save as Virtual Database menu item to save the virtual database.

1. Virtual databases are available for revisiting in your "My Data" list.
2. What is actually saved are the filters; the next time you access this database the filters are recomputed to show the sequences.
   1. Therefore the sequences you view upon revisiting may be different from the ones you had the first time, due to database upgrades.
3. Virtual reference databases are also available in the list of "My databases" in the Blast workflow.
4. Saving virtual databases of your own reads is very similar but can get complicated in terms of choosing the reads databases to browse. To see more details see the virtual reads database page.

View menu

Using items in this menu you can change the columns displayed on the web browser when viewing the result.

1. My views: As shown in the figure above, this item scrolls horizontally to show all views saved by the user. To choose one of these previously saves views, simply click on it.
2. Save view: choose this item to save the current view. Such a saved view keeps track of the columns that are currently being displayed. Upon choosing this item, a window pops up which allows you to give this view a name - or to replace an existing view with this one.
   
3. Delete View: opens a pop-up which allows you to specify a previously saved view you want to delete.
4. Define Columns: this is the first step in defining a new view. Upon choosing this pops a window which shows a shuttle with all available columns in the left side and all columns being displayed on the right.
   
   * In order to add a column to display, select it in the Left set and press the >> button.
   * To remove a column from display, select it in the Right set and press the << button.
   * To move a displayed column leftward, select it int he right set and click the up button and
   * To move a column rightward, select it in the right set and click the down button.
   * Once you are satisfied with your selections, click the Apply button.
   NOTE: Once a new view is so defined by selecting the columns to show, you can then save it as a new view and it becomes available in the My views list mentioned above.
5. Show only checked results: You can select specific results by clicking the checkbox next to them. Then, choosing this item removes all unchecked results from view, displaying only the checked ones.
6. Show only new subjects: For IP searches, there is a re-do function that allows you to run the same search with different parameters and / or different subject databases. In the case of such redo's, it is often useful to be able to see what is new i.e. results found int he new search that were not present in the old search. Selecting this menu item shows only the new results.
7. Expand all: All results are initially shown in condensed table form. However, clicking them expands the result to see (a) alignment or (b) annotation of subject sequence or (c) subject sequence or (d) query sequence. This menu item allows you to expand the corresponding item for ALL results in present display without having to select that expansion for each result.
   

Export

This menu allows you to export the results in a variety of formats. If you have selected some results using check-boxes, a pop-up dialog clarifies whether you want to export all results or just the selected ones.

Create reports

1. Document: Current view. This creates an html report (which you can conveniently open in any word processor like Word). The report contains an audit trail of how the document was generated, and full annotation of all results.
   1. NOTE: When the number of results exported into a document is very high, the file size is large and the word processor can take a long time to open it. In these cases, you have three choices: (a) apply some filters to reduce the number of your results or (b) use a table format report or (c) use an html export format so that it opens up in your web browser (which is often more robust than word processor programs.
2. GFF. Exports results in GFF (General Feature Format).
3. Table: Current view. This creates an html table (which you can conveniently open in any spreadsheet program like Excel) containing all the entries from the table you view on the web browser.
   1. This report is generally much more concise than the document report and hence, you can create this for a larger number of results.
   2. You can change how the table looks by changing the view (as explained above) on your web browser before running this report.
4. Special reports. Some special reports which are most useful for patent searches:
   1. PN List. In this report, you just get a list of all patent numbers included in the result (one PN per line in a table).
   2. PN + Family List. In this report, you get a list of all patent numbers included in the result along with all members of each PN's family (one PN per line in a table).

Note: Patent Statistics report is also a special report of particular interest to users doing patent searches with multiple query sequences. This report is available from the Applications menu as explained below. To get this report, click Applications -> Patent statistics.

Export sequences

When browsing results from a sequence search, note that a result really is a query-subject pair. So, you will also need to specify whether you want to export the queries, subjects or both. The export can be done in standard formats like fasta, EMBL and a format that looks like a Genbank file.

Applications

Several applications (many not native to GenomeQuest) can be launched from the applications menu - one of the reasons that GenomeQuest is a true sequence data management platform. Some example applications are found under the Applications menu. Please note

• This list of applications will evolve constantly based on user requirements.
• If you would like to see your favorite sequence analysis application here, please us know.

Pop-up Dialog

When you choose an application from this menu, a dialog box pops up which allows you to choose whether you want to run the application on just the selected (using check-boxes) sequences or all the sequences.

Just like with Export, when using Applications on results from a sequence search, you will need to specify which sequences to send to the application: only the query sequences, only the subjects or both.

Typically, the dialog box also has a link to Advanced options. Click this link to see and manipulate some parameters for the application. These parameters are application specific.

Limits

Most applications have limits on the number of sequences they can handle. For example, you cannot run ClustalW on 10 million sequences. The limit is Application-specific.

GenomeQuest imposes this application-specific limit on the number of sequences which are exported into an application. To be within the limit you can

• apply some filters to bring down the number of sequences in your list.
• use check-boxes and select the specific sequences to export and then specify Selected results in the pop-up dialog.

If you do not use either of the above methods, then GenomeQuest simply chooses the top X results to export (where X is the application-specific limit).

List of available applications

The following applications are run on GenomeQuest servers and do not have additional pre-requisites:

1. Assembly: Exports sequences to the Newbler Assembler to do a de novo assembly of the selected sequences.
2. Emboss: Several utilities from the EMBOSS suite are listed here.
3. Extract: a set of utilities for exporting sequence sets like queries and those queries that did not have any hits (and hence will not be visible in the display). These utilities are especially useful when the number of query sequences in the search is very large.
4. Sequence Search: Export sequences into GenomeQuest's Sequence Search page.
5. ClustalW: Export sequences into this multiple sequence alignment software.
6. UCSC Genome Browser: Export sequences to this viewer.
   1. Only available on results when a sequence search is done against the human genome.
7. Patent statistics: This is a special report which provides patent overview.
   1. This report is only available from results of a sequence search (not annotation search).
   2. It is useful when there are multiple query sequences and patents are in the subject databases.

The following are dektop applications. To export to them, you naturally need to have these packages installed on your desktop.

1. Geneious: Exports sequences to the desktop application Geneious, by BioMatters. This is a sequence analysis package with advanced functionalities such as Primers design, contigging, annotation editing and multiple alignment. You can download a trial version of Geneious. GenomeQuest can provide a Geneious plugin so that you can export sequences from Geneious directly to GenomeQuest. Click here to download and install the GQ plugin for Geneious (you need Geneious installed).
2. Invitrogen: Exports sequences to the desktop application Vector NTI, by Invitrogen, for sequence analysis (Vector NTI web page). We also provide a Vector NTI plugin so that you can export sequences from Vector NTI directly to GenomeQuest. Click here to download and install the GQ plugin for Vector NTI (you need Vector NTI installed).
3. BizInt SmartCharts: Export results into BizInt.
   1. Useful for sequence searches against patent databases.