BRF-Software - User contributions [en]

O2DBIWiki

2012-02-17T08:29:27Z

Agoesman:

__NOTOC__
= O2DBI Overview Page =

== O2DBI - Introduction ==

O2DBI is a codegenerator for SQL-based data management layers. Based in a description of class hierarchies, it produces ready-to-use perl classes for storing and retrieving data.

Main features:
* support for arbitrary complex class hierarchies
* polymorphic queries within class hierarchies
* easily extensible classes without adding another layer
* simple interface
* XML based description of classes

O2DBI is used in nearly all applications developed at the [http://www.cebitec.uni-bielefeld.de/groups/brf/software/ CeBiTec].



== Documentation ==

* Introduction
** [[O2DBIWiki/IntroScope| The scope of O2DBI]]
** [[O2DBIWiki/IntroFeatures| O2DBI Features]]
** [[O2DBIWiki/ORMapping| Object-relational mapping]]
** [[O2DBIWiki/IntroRequirements| Requirements]]
* Working with O2DBI
** [[O2DBIWiki/WorkingDesigner| The O2DBI Designer]]
** [[O2DBIWiki/WorkingXMI| Converting XMI files]]
** [[O2DBIWiki/WorkingGenerator| Generating perl code]]
* Using the generated code
** [[O2DBIWiki/CodeOverview| Overview of the generated modules]]
** [[O2DBIWiki/CodeBackend| Backend - connecting to databases]]
** [[O2DBIWiki/CodeMaster| Master - central instance]]
** [[O2DBIWiki/CodeClasses| Classes - the generated interface]]
** [[O2DBIWiki/CodeExtensions| Extending the generated interface]]
* [[O2DBIWiki/FeaturesTODO| Features and TODO]]
* [[O2DBIWiki/FAQ| FAQ]]












Author: [http://www.cebitec.uni-bielefeld.de/~blinke Burkhard Linke]

GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog

2011-11-30T10:37:16Z

Agoesman:

= Annotation Dialog =

In this section the manual annotation of a Region using the Web Interface is
described. A description of the terms and concepts of the GenDB annotation
concept can be found in the [[GenDBWiki/TermsAndConcepts/AnnotationConcepts|Annotation Concepts]] of the [[GenDBWiki/TermsAndConcepts|Terms and Concepts Section]]

Two kinds of annotations do fully characterize a region:

* A Region Annotation
* A Function Annotation

== Region Annotation ==

The following image shows the annotation dialog of the GenDB Web interface.
The first line informs about the region name and - if available - the biological
name of the region. On both sides of this line there are arrows to access the
previous or the following of the current region.

On the left side, the list of functional and regional annotations is located.
The selected annotation is marked in blue and shown on the right side in the
Annotation Detail section. In this case, it is a regional annotation done by the
Critica auto annotator.

In the two drop down menues 'Set regional status to' and 'Set functional status to'
a number of stati for the two different annotation types can be chosen. A completely
annotated coding sequence should have the two stati shown here which is 'finished'
for the regional and 'annotated' for the functional annotation.

Following the date and the annotator (which can be a human or an autoannotator) the
start and the stop position of the region are displayed. These can be changed in the
[[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]].

After the description field and the comment field there are the observations that
leaded to the current annotation listed. The following field contains additional
observations that can be added to the list via the buttons 'Show selected ...' to look
at selected observations or 'Add observations...' to add them manually to the list.

The last section shows links for the current annotation. New links can be added in the
field right to the links.

On the bottom and on the top of the Annotation Dialog there are three buttons, respectively.
These have the functions to add a new annotation ('Add new') or accept an annotation (which
means the same as 'Add new' but the regional status is automatically set to 'finished' and
the functional status is automatically set to 'annotated'). To make no changes and just
close the annotation dialog press the 'Close' button.

[[File:AnnotationRegion.png|Screenshot of the Region Annotation Dialog.]]

== Function Annotation ==

Choosing a functional annotation on the left side a number of additional fields occur on
the right side. One additional field is an entry for the gene name for coding regions which
is a biological identifier for the region. A certain gene name should only be given once
for a genome.

Right from the gene name entry there is the possibility to add GeneOntology numbers as a
functional classification for the gene. More information to each GO number can be accessed
via the links next to the field.

The EC-Number entry can contain one Enzyme Commission number that is a numerical classification
scheme for enzymes. Genes that do not code for enzymes do not get such a number. The EC numbers
can be used for the reconstruction of the metabolic pathways of the organism e.g. in [[GenDBWiki/WebDocumentation/MainViews/KEGGView|KEGG]].

In the Gene Product field the gene is shortly characterized. If there is no exact characterization
possible, there are different types of classes available for a gene product. These can be
accessed in the drop down menu below the Gene Product entry and is entered in the entry after
choosing one. Examples are 'hypothetical protein' if no further information is available for
the gene product or 'conserved hypothetical protein' if there is at least one good hit to
a protein in another organism.

The Description field of the functional annotation is a further detailed characterization of
the gene product. It is exported to the EMBL output of the genome. This is not the case
for any entries in the Comment field.

Below the description field there is the check box 'Experimental' which should be clicked if any
of the results of the annotation are verified in the wet lab. Following are entries concerning
the COG (Cluster of orthologous group) functional classification, namely the COG number, COG
funccat ID and COG funccat Description. These fields cannot be edited manually, but only
pressing the button 'Get' on the right. In the upcoming dialog a COG number can be selected and
the entries will be filled.

In the 'Function' field a short description of the function of the gene can be inserted.
A confidence for the complete annotation is also to be entered in the respective drop down field.
There are different confidence stati that can be chosen here. The strongest confidence is
'High confidence in function and specificity' and the weakest is 'Hypothetical protein'.

The following fields have already been described for the Region Annotation.

[[File:AnnotationFunction.png|Screenshot of the Function Annotation Dialog.]]

File:AnnotationFunction.png

2011-11-30T10:35:50Z

Agoesman: Screenshot of the GenDB Function Annotation Dialog.

Screenshot of the GenDB Function Annotation Dialog.

File:AnnotationRegion.png

2011-11-30T10:35:21Z

Agoesman: Screenshot of the GenDB Region Annotation Dialog.

Screenshot of the GenDB Region Annotation Dialog.

GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog

2011-11-30T10:30:02Z

Agoesman:

= Show Sequence Dialog =

This dialog shows a graphical representation of the sequence of a region. In the middle of the window, you can find both strands of the DNA
sequence of the region. Above and below these two DNA strands the translated protein sequences can be found. There are 3 protein strands for
each DNA strand, as each reading frame is of the DNA is translated.

Some DNA bases or amino acids have a different background color. Here, special sequences are highlighted, e.g. all DNA triplets that represent
a start codon in the frame of the displayed region is shown in green background color (1), the corresponding amino acid is underlied in brown (2).

[[File:ShowSequenceDialog.png|Screenshot of the Show Sequence dialog.]]

The protein sequence that belongs to the region is shown in a box in red color (3). The prepending amino acids have a blue background color (4),
as it could belong to the protein if the start codon should be changed.

Highlighted in brown background color are DNA bases that represent a ribosomal binding site (5).

File:ShowSequenceDialog.png

2011-11-30T10:29:20Z

Agoesman: Screenshot of the GenDB Show Sequence Dialog.

Screenshot of the GenDB Show Sequence Dialog.

GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog

2011-11-30T10:26:39Z

Agoesman:

= Create Region Dialog =

This dialog gives the user the ability to create regions that have not been created automatically in GenDB.

[[File:RegionCreator.png|Screenshot of the Region Creator Dialog.]]

Enter start and stop position in basepairs to create a new region on the current contig. You have to select the type of the region
from the GenDB region class hierachy list box on the left. GenDB will create an initial regional annotation for this region.

The next step of the region creation process is to select a set of applicable tools that will compute observations on this region.
Deselect the checkbox left to the toolname to avert a tool to be started.

To check the state of the tools started for this region use (Re)start tools later on.

File:RegionCreator.png

2011-11-30T10:25:22Z

Agoesman: Screenshot of the GenDB Region Creator Dialog.

Screenshot of the GenDB Region Creator Dialog.

GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer

2011-11-30T10:19:35Z

Agoesman:

__NOTOC__
= Sequence Viewer =

The Sequence Viewer (available since GenDB 2.4) allows a zoomed view into the genomic sequence along with its six translated frames.
You can easily '''''select''''' some sequence, afterwards copy it with '''''Control+C''''', and finally paste it with '''''Control+V''''' into an arbitrary place.

Pressing the Show Sequence button in the main window of GenDB, will display the [[SequenceViewer]]. Green rectangles represent the CDS. The CDS that is activated in GenDB has a stronger border and a brighter green color (directly reachable with the '''''Center''''' button). CDS that are marked as ignored are dashed and grey. Moving the mouse over a CDS, displays its details into the '''''Region-Information''''' table. The [[SequenceViewer]] allows you to scroll within a 6000nt-window. In order to get the next or previous 6000nt of the contig press the '''''Left''''' or '''''Right''''' button. Thus, its possible to walk easily through the whole contig.

Selecting any sequence will display the selected sequence at the '''''Sequence-Editor'''''. If you select some sequence on the back strands, a '''''Reverse''''' button allows you to reverse the selected sequence, in order to obtain the sequence in the biological right direction. Afterwards you can select this sequence, copy and paste it into e.g. a file.

=== How to select a sequence ===
The behaviour of the [[SequenceViewer]] is similar to common text-editors (e.g. notepad). You have two possibilities to select an arbitrary sequence:
* Press the left mouse button and move it to the right or to the left (recommeneded for short sequences)
* ''Left-Click'' on the start character, move the scroll bar, ''Shift+Left-Click'' on the end character (recommeneded for long sequences)

In order to obtain quickly the whole sequence of a CDS:
* Move the mouse to the left border of a CDS, ''Left-Click'' and pull the mouse slightly under

[[File:SequenceViewer.png|Screenshot of the GenDB Sequence Viewer.]]

File:SequenceViewer.png

2011-11-30T10:18:52Z

Agoesman: Screenshot of the GenDB Sequence Viewer.

Screenshot of the GenDB Sequence Viewer.

GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate

2011-11-30T10:17:20Z

Agoesman:

__NOTOC__
'''This method considers for a subset of the CDS-regions (of a contig) whether significant functional observations of a specified tool exist that are not yet used in the functional annotation of the CDS-regions.'''

=== Introduction ===
----
'''Supporting Observations''': Functional Annotations of a region object (e.g. a CDS region) considerably rely on information that is provided by precomputed functional observations of various tools suitable to detect functional characteristics. For example Blast tools may detect homology information for a regions's sequence that allows you to infer some functional meaning of the region object (e.g. what kind of gene it is!). It's useful to list those related observations in the framework of the functional annotation. Observations listed as attributes of the annotation object are referred to as ''supporting observations''. They serve to provide evidence to the content of the annotation.
----

'''This method serves two aspects in managing the supporting observations of the CDS-regions of a contig:'''

It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the ''supporting observations'' that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation (including the best currently used supporting observation for that tool-if it exists) and finally the up-to-date most promising candidate observation to improve evidence of the annotation . A html-link allows you to get quickly into the annotation dialog of that gene.

Additionally it's possible to enrich the result-list by observations that are proposed as the currently best candidates to be used in the annotations when there haven't been used any supporting observations yet!

[[File:SuppObsUpdate.png|Screenshot of the gene annotation update wizard.]]

=== General settings ===

'''The CDS-regions will be taken from the contig, that is currently selected in the session!'''

'''Select from Blast-tools:'''
Here you can choose a specific Blast tool from a list of all available Blast tools in the project's database.

'''Number of regions to be processed'''
'''at once (size of interval):'''
The programm will take this setting as the number of CDS-regions that are processed at once (called size of interval)!

'''Change stepping size:'''
Here you can change the interval size.

'''Select range of CDS-regions to be processed:'''
The overall set of CDS regions can be seen as a sorted list of genes [gene_1 ... gene_N] that is divided for computational reasons into a subset of intervals (e.g. when the interval size is ''50'' you will get intervals like ''gene_1 .. gene_50'', ''gene_51 .. gene_100'' and so on). This allows you to process small subsets of the genes in an ordered fashion!

'''Propose all:'''
Check out this box if you want the programm to propose candidate observations for functional annotations even though there haven't been used any supporting observations so far! This helps you to complete genome annotation.

'''Compute results for settings:'''
This will start the computation!

=== Interpreting the results ===

'''Following is an overview of the most important elements (column names) of the single entries in the result-list:'''

'''CDS_NAME''': Examined gene. The name is also a link to the referred region in the main window of gendb.

'''CURRENT_BEST_EVALUE''': Evalue of the best (currently used) supporting observation (corresponding to the specified tool).

'''CURRENT_BEST_SCORE''': Score of the best (currently used) supporting observation (corresponding to the specified tool).

'''CURRENT_BEST_DESCR''': Description of the best (currently used) supporting observation (corresponding to the specified tool).

'''CURRENT_BEST_DATE''': Date of the best (currently used) supporting observation (corresponding to the specified tool).

'''CURRENT_AnnF_DESC''': Description of the current annotation function.

'''CURRENT_AnnF_DATE''': Date of creation of the current annotation function.

'''PROPOSED_EVALUE''': Evalue of the proposed observation.

'''PROPOSED_SCORE''': Score of the proposed observation.

'''PROPOSED_DESCR''': Description of the proposed observation.

'''PROPOSED_DATE''': Date of creation of the proposed observation.

'''ACTIONS''': Opens the annotation dialog.

'''ANNOTATOR''': Name of the annotator that created the current annotation function.

File:SuppObsUpdate.png

2011-11-30T10:15:13Z

Agoesman: Screenshot of the GenDB Gene Annotation Update Wizard.

Screenshot of the GenDB Gene Annotation Update Wizard.

GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector

2011-11-30T10:09:26Z

Agoesman:

__NOTOC__
'''SNP-Detector detects and lists Single Nucleotide Polymorphisms in genomic data.'''

''Single Nucleotide Polymorphisms'' (abbreviated SNPs,pronounced "snips") are a phenomenon related to homologous sequences. They describe little (regularly only one base is affected) differences between strongly related, homologous sequences. SNPs may fall within coding sequences (CDS) of genes or between genes (intergenic regions). SNPs are due to single nucleotide mutations (substitution, deletion or insertion of a single nucleotide) which may happen independently on the single sequences. Normally, for a variation to be considered a SNP, it must occur in at least 1% of the population. SNP-Detector, though, is not to be seen in the context of this statistical approach, but reports all single nucleotide variations between homologous sequences (CDS-regions or intergenic regions) of two contigs belonging to strongly related organisms.

SNPs are important features of a genomic sequence. Their distributions are normally characteristic for a specific strain. SNPs are often used for rapid classification of an organism. Since SNPs in CDS sequences may change codons they can also differ the function of genes and therefore be responsible for altered phenotypical characteristics of mutants. A convenient method for detecting SNPs is restriction fragment length polymorphism (SNP-RFLP).


== Starting SNP-Detector and general remarks ==

As described above SNP-Detector can be used to list all single nucleotide variations between two strongly related contigs. This is achieved by analyzing blast-results computed for the sequences (CDS or intergenic regions) of one contig (named "source" in the following) against the corresponding sequences of another (strongly related) contig (named "target" in the following). SNP-Detector therefore relies on the results of BLAST-tools from the projects database which already have to be run for the contigs in a former stage as a precondition.
----

To open the SNP-Detector configuration page you have to select the option "SNP Detection" from the category "Edit" in the main menue. A new window will be opened and you will see the configuration page.

----
'''''Notice, that SNP-Detector may be run for both types of sequences, CDS and intergenic regions, independently!'''''


== Configuring SNP-Detector ==

[[File:SNP-Detector-Config.png|Screenshot of the SNP Detector configuration dialog.]]

----
Options:

'''Mode selection:'''
On the configuration page the user can choose whether he wants SNP-Detector to be run for CDS regions or intergenic regions only, or for both. You simply have to check out the corresponding boxes named "SNPs in CDS" or "SNPs in intergenic regions", respectively.

'''The following options are similar in both modes and will therefore be explained only once!'''

'''Selecting a contig:'''
Depending on what mode you have selected you can now select a contig object from the projects database. This contig must be regarded as the "source" contig (concerning the term "source contig" in this context see also section [[#StartingSNPDetection|general remarks]]), that means, that the BLAST tool you will select in a following step must have been executed on this contig!

'''Selecting a BLAST tool:'''

Here you can select a suitable tool for your purpose. That means, that the tool's predefined database must be related to the "target" contig (see also section [[#StartingSNPDetection|general remarks]]), since its results where computed for the "source" contig and therefore the combination makes sense.

When you are ready you can submit the page!

----
EXAMPLE FOR CORRECT USE:

The BLAST-tool "Blast2n_vs_NC_YYYY" with its predefined database "NC_YYYY.cds" was run on contig NC_XXXX!
In this case NC_XXXX is the "source" contig, whereas "NC_YYYY" is said to be the "target" contig. Therefore you would select the tool's name from the popup-menue and choose the contig "NC_XXXX" from the popup-menue displaying all contigs in the project!
----

'''NOTE THAT THE NAME OF THE SELECTED BLAST-TOOL MUST NOT CONTAIN BLANKS!'''
'''''This is due to the fact, that the processing is made on the cluster and this is a restriction which momentarily has to be made. You ought to keep this in mind, when you create your tools.'''''

'''''The intergenic regions are not region objects in GENDB as for example CDS regions are. They are only computed for the BLAST step and will not be stored in the project's database! That is why you have to use a specific BLAST-tool belonging to the class GENDB::Intergenic_Blast!'''''

== SNP-Detector is running ==

When you have submitted the configuration and the tool's checks does not detect any problems you will be informed that your job is in process. Please keep this information page open, since it will show the results later on. Since SNP-Detector checks all the sequences of the contig the computation may last a period of time.

== SNP-Detector overview page ==

When SNP-Detector performed the computation you will be redirected to an overview page containing links to your results for CDS regions or intergenic regions (depending on your settings in the former stages).

Now, go on by clicking on of the links to your results!

[[File:SNP-Detector-Results.png|Screenshot of the SNP Detector result overview.]]
----
'''''PLEASE NOTE, that you should not close this page unless you want to discard all your results. As long as the overview page is open and your session does not expire your results remain accessible from that overview page.'''''

== Result pages ==

The result page shows the single results for all CDS regions or intergenic regions. The representation of the results differs for CDS regions and intergenic regions. See the appropriate section in this manual to get to know what the entries (single rows) in your result lists mean! To distinguish between "source" (1) and "target" contig (2) numbers were introduced that are appended on the column names as suffixes. Their meaning can be regarded as distinguishing between features related to "region 1" ("source") or "region 2" ("target"), respectively.

----
'''CDS Regions:'''
You will see the names of the two CDS regions (on "source" and "target" contig) that are most likely to be homologous as calculated from the available BLAST results. These names represent links that will direct you to the corresponding objects in GENDB. You also see the PERCENT IDENTITY of the hit and the LENGHT of the hit.
If you actually want to see an overview of the detected SNPs you must click on the link named "Show Report". The link "Show Alignment" will direct you to a new window where you can see the alingment of the two sequences.
-----
'''Intergenic regions:'''
First you see a name for the intergenic region. This name is arbitrary and merely represents a counter for the regions. ''The intergenic regions are not region objects in GENDB as for example CDS regions are. They are only computed for the BLAST step and will not be stored in the project's database! That is why you have to use a specific BLAST-tool belonging to the class GENDB::Intergenic_Blast!''

You will see the names of the determined left and right flanking CDS regions (on "source" and "target" contig) for the intergenic regions that are most likely to be homologous as calculated from the available BLAST results. These names represent links that will direct you to the corresponding objects in GENDB. You also see the PERCENT IDENTITY of the hit and the LENGHT of the hit.
If you actually want to see an overview of the detected SNPs you must click on the link named "Show Report". The link "Show Alignment" will direct you to a new window where you can see the alingment of the two sequences.
----
[[File:SNP-Detector-List.png|Screenshot of the SNP Detector result list.]]
----
It's possible to navigate through the result list. Closing the result page including the result list is no problem, since you can revisit the page from the overview page!

Closing the overview page:
Since SNP-Detector stores its intermediate results in files you will get an information message that these files are deleted. This is normal!
----

[[Category:Homepage]]

File:SNP-Detector-List.png

2011-11-30T10:05:44Z

Agoesman: Screenshot of the GenDB SNP Detector Result List window.

Screenshot of the GenDB SNP Detector Result List window.

File:SNP-Detector-Results.png

2011-11-30T10:05:09Z

Agoesman: Screenshot of the GenDB SNP Detector Results Overview page.

Screenshot of the GenDB SNP Detector Results Overview page.

File:SNP-Detector-Config.png

2011-11-30T10:04:21Z

Agoesman: Screenshot of the GenDB SNP Detector Configuration Dialog.

Screenshot of the GenDB SNP Detector Configuration Dialog.

GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog

2011-11-29T20:57:50Z

Agoesman:

= The Configuration Dialog =

The user settings for the complete GenDB web interface can be edited in this dialog. This includes colors, numbers of observations for different tools
you want to view and many other things. The navigation is done by the six links at the beginning which represent the main menu of the !ConfigurationDialog.
These six menues are now shortly described.

== GC-Plot ==

[[File:Config-GCPlot.png|Screenshot of the GenDB GC Plot Configuration Dialog.]]

== Observations ==

Define the colors for the five quality levels and the way observations
will be sorted by default

[[File:Config-Observations.png|Screenshot of the GenDB Observations Configuration Dialog.]]

== Tool results ==

[[File:Config-ToolResults.png|Screenshot of the GenDB Tool Results Configuration Dialog.]]

Define the number of observations for each tool/ tool class to
be displayed. These settings will affect the way observations
are displayed in the [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Dialog]]

Use the following convention:

* -1 = show all
* 0 = show none
* >0 = show limited amount

== Contig View ==

[[File:Config-ContigView.png|Screenshot of the GenDB Contig View Configuration Dialog.]]

This configuration tabsheet affects the colors and the way
regions are displayed in the [[GenDBWiki/WebDocumentation/MainViews/ContigView|Contig view]].
For every region type color, arrow and visibility can be specified. The way regions are colored
depends on the selection:
* region status: use the colors defined in the section Region Status. Each region will be filled according to its regional status
* function status: use the colors defined in the section Function Status. Each region will be filled according to its functional status
* region type: use the colors defined in the section Region Color.

== Search Patterns ==

[[File:Config-SearchPatterns.png|Screenshot of the GenDB Search Patterns Configuration Dialog.]]

If you define a pattern here, the RBS finder will use it to
detect ribosomal binding sites.

== Preferences Management ==

[[File:Config-PrefManagement.png|Screenshot of the GenDB Preferences Management Configuration Dialog.]]

Download the current settings in a INI-formated
textfile or revert to the default settings.
It is also possible to upload your own configuration files.

File:Config-PrefManagement.png

2011-11-29T20:52:11Z

Agoesman: Screenshot of the GenDB Preferences Management Configuration Dialog.

Screenshot of the GenDB Preferences Management Configuration Dialog.

File:Config-SearchPatterns.png

2011-11-29T20:51:43Z

Agoesman: Screenshot of the GenDB Search Pattern Configuration Dialog.

Screenshot of the GenDB Search Pattern Configuration Dialog.

File:Config-ToolResults.png

2011-11-29T20:51:16Z

Agoesman: Screenshot of the GenDB Tool Results Configuration Dialog.

Screenshot of the GenDB Tool Results Configuration Dialog.

File:Config-Observations.png

2011-11-29T20:50:48Z

Agoesman: Screenshot of the GenDB Observations Configuration Dialog.

Screenshot of the GenDB Observations Configuration Dialog.

File:Config-ContigView.png

2011-11-29T20:50:08Z

Agoesman: Screenshot of the GenDB Contig View Configuration Dialog.

Screenshot of the GenDB Contig View Configuration Dialog.

File:Config-GCPlot.png

2011-11-29T20:49:34Z

Agoesman: Screenshot of the GenDB GC Plot Configuration Dialog.

Screenshot of the GenDB GC Plot Configuration Dialog.

GenDBWiki/WebDocumentation/DialogWindows/ComputeJobStatistics

2011-11-24T15:29:01Z

Agoesman:

== Compute Job Statistics ==

[[File:ComputeJobStatistics.png|Compute Job Statistics Dialog.]]

File:ComputeJobStatistics.png

2011-11-24T15:28:38Z

Agoesman: Screenshot of the GenDB Compute Job Statistics Window.

Screenshot of the GenDB Compute Job Statistics Window.

GenDBWiki/WebDocumentation/DialogWindows/ComputeJobStatistics

2011-11-24T15:26:46Z

Agoesman: Created page with "== Compute Job Statistics == Compute Job Statistics Dialog."

== Compute Job Statistics ==

[[File:ComputeJobsStatistics.png|Compute Job Statistics Dialog.]]

GenDBWiki/WebDocumentation/DialogWindows

2011-11-24T15:26:00Z

Agoesman:

__NOTOC__
= GenDB Dialog Windows =

The GenDB Web interface handles a lot of basic functions using dialog windows.
Here, the dialogs are listed and explained.

* [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Window]]
* [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SearchDialog|Search Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/PatScan|PatScan Search]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CircularPlot|Circular Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/WholeGenomePlot|Whole Genome Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ReportDialog|Region Report]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|DNA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ZoomRegionDialog|Region Zoom]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog|Configuration Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|Region Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportCDS|CDS Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportGenBankEMBL|EMBL and GenBank Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|Multiple Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutation|Mutation Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/Virtual2DGel|Virtual 2D Gel Browser]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|Genetic Code Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|Organism and Strain Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/BlastInterface|Blast Interface]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator|Comparative Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ClusterTool|Gene Cluster Tool]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate|Supporting Observations Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector|SNP Detector]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ToolStatus|Tool Status Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComputeJobStatistics|Compute Job Statistics Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteContig|Delete Contig Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteRegion|Delete Region Dialog]]

GenDBWiki/WebDocumentation/DialogWindows/WholeGenomePlot

2011-11-24T15:24:34Z

Agoesman: Created page with "== Whole Genome Plot == GenDB Whole Genome Plot."

== Whole Genome Plot ==

[[File:WholeGenomePlot.png|GenDB Whole Genome Plot.]]

File:WholeGenomePlot.png

2011-11-24T15:23:35Z

Agoesman: Screenshot of the GenDB Whole Genome Plot.

Screenshot of the GenDB Whole Genome Plot.

GenDBWiki/WebDocumentation/DialogWindows

2011-11-24T15:19:07Z

Agoesman:

__NOTOC__
= GenDB Dialog Windows =

The GenDB Web interface handles a lot of basic functions using dialog windows.
Here, the dialogs are listed and explained.

* [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Window]]
* [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SearchDialog|Search Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/PatScan|PatScan Search]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CircularPlot|Circular Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/WholeGenomePlot|Whole Genome Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ReportDialog|Region Report]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|DNA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ZoomRegionDialog|Region Zoom]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog|Configuration Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|Region Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportCDS|CDS Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportGenBankEMBL|EMBL and GenBank Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|Multiple Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutation|Mutation Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/Virtual2DGel|Virtual 2D Gel Browser]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|Genetic Code Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|Organism and Strain Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/BlastInterface|Blast Interface]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator|Comparative Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ClusterTool|Gene Cluster Tool]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate|Supporting Observations Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector|SNP Detector]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ToolStatus|Tool Status Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteContig|Delete Contig Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteRegion|Delete Region Dialog]]

GenDBWiki/WebDocumentation/DialogWindows/DeleteRegion

2011-11-24T15:09:41Z

Agoesman: Created page with "The button for deleting regions is only displayed for project maintainers, developers, and chiefs (see also GenDB rights and roles). [[File:DeleteRegion.png|GenDB Delete Region ..."

The button for deleting regions is only displayed for project maintainers, developers, and chiefs (see also GenDB rights and roles).

[[File:DeleteRegion.png|GenDB Delete Region Dialog.]]

File:DeleteRegion.png

2011-11-24T15:09:17Z

Agoesman: Screenshot of the GenDB dialog for deleting single regions.

Screenshot of the GenDB dialog for deleting single regions.

GenDBWiki/WebDocumentation/DialogWindows

2011-11-24T15:07:09Z

Agoesman:

__NOTOC__
= GenDB Dialog Windows =

The GenDB Web interface handles a lot of basic functions using dialog windows.
Here, the dialogs are listed and explained.

* [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Window]]
* [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SearchDialog|Search Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/PatScan|PatScan Search]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CircularPlot|Circular Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ReportDialog|Region Report]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|DNA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ZoomRegionDialog|Region Zoom]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog|Configuration Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|Region Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportCDS|CDS Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportGenBankEMBL|EMBL and GenBank Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|Multiple Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutation|Mutation Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/Virtual2DGel|Virtual 2D Gel Browser]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|Genetic Code Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|Organism and Strain Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/BlastInterface|Blast Interface]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator|Comparative Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ClusterTool|Gene Cluster Tool]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate|Supporting Observations Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector|SNP Detector]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ToolStatus|Tool Status Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteContig|Delete Contig Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteRegion|Delete Region Dialog]]

GenDBWiki/WebDocumentation/DialogWindows/BlastInterface

2011-11-24T15:04:00Z

Agoesman:

__NOTOC__
= Blast Interface =
 
The Blast Interface can be used to blast DNA or AA sequences vs. global databases (like NR, SWISSPROT...) or vs. private databases like the contigs in the selected project. You can use different Blast-Algorithms here:
* '''blastp:''' to blast a protein-sequence vs. a protein-database
* '''blastn:''' to blast a DNA-sequence vs. a DNA-database
* '''blastx:''' to blast a DNA-sequence vs. a protein-database - the DNA-sequence is translated in all six reading frames
* '''tblastn:''' to blast a protein-sequence vs. a DNA-database - the protein database is translated dynamically in all six reading frames
* '''tblastx:''' to blast a translated DNA-sequence vs. a translated DNA-database
* '''psiblast:''' to blast a protein-sequence vs. a protein-database. psiblast uses position-specific-score-matrices to score matches, it may be more sensitive

You can choose different databases according to the algorithm you selected.
The input-sequence can be copied into the text-field or you can load a query file from your disk. 
Other options are explained [http://www.ncbi.nlm.nih.gov/blast/ here].

[[File:BlastSearch.png|GenDB Blast Search Dialog]]

When you made all your choices you can start the BLAST-run by clicking "Submit". You will see the following page as long as the result is being computed:

[[File:BlastSearchWait.png|GenDB Blast Search Dialog waiting for job execution.]]

File:BlastSearchWait.png

2011-11-24T15:01:22Z

Agoesman: Screenshot of the GenDB Blast Search Dialog while waiting for job execution.

Screenshot of the GenDB Blast Search Dialog while waiting for job execution.

File:BlastSearch.png

2011-11-24T15:00:32Z

Agoesman: Screenshot of the GenDB Blast Search Dialog.

Screenshot of the GenDB Blast Search Dialog.

GenDBWiki/WebDocumentation/DialogWindows/ExportGenBankEMBL

2011-11-24T14:08:54Z

Agoesman: Created page with "GenDB EMBL and GenBank export dialog."

[[File:ExportGenBankEMBL.png|GenDB EMBL and GenBank export dialog.]]

GenDBWiki/WebDocumentation/DialogWindows

2011-11-24T14:07:39Z

Agoesman:

__NOTOC__
= GenDB Dialog Windows =

The GenDB Web interface handles a lot of basic functions using dialog windows.
Here, the dialogs are listed and explained.

* [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Window]]
* [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SearchDialog|Search Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/PatScan|PatScan Search]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CircularPlot|Circular Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ReportDialog|Region Report]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|DNA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ZoomRegionDialog|Region Zoom]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog|Configuration Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|Region Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportCDS|CDS Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportGenBankEMBL|EMBL and GenBank Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|Multiple Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutation|Mutation Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/Virtual2DGel|Virtual 2D Gel Browser]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|Genetic Code Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|Organism and Strain Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/BlastInterface|Blast Interface]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator|Comparative Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ClusterTool|Gene Cluster Tool]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate|Supporting Observations Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector|SNP Detector]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ToolStatus|Tool Status Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteContig|Delete Contig Dialog]]

File:ExportGenBankEMBL.png

2011-11-24T14:06:14Z

Agoesman: Screenshot of the GenDB EMBL or GenBank export dialog.

Screenshot of the GenDB EMBL or GenBank export dialog.

GenDBWiki/WebDocumentation/DialogWindows/ExportCDS

2011-11-24T14:05:26Z

Agoesman:

= Export CDSs Dialog =

Use this dialog to export all coding regions of a contig as FASTA files. You have the choice between AA-sequence, DNA-Sequence and plain text CDS information.
'''NOTE:''' This function requires a huge amount of processing power and time. So it may take a while until you can download the FASTA files.

[[File:ExportCDS.png|CDS export dialog.]]

File:ExportCDS.png

2011-11-24T14:02:57Z

Agoesman: Screenshot of the GenDB CDS Export Dialog

Screenshot of the GenDB CDS Export Dialog

GenDBWiki/WebDocumentation/DialogWindows/DeleteContig

2011-11-24T14:02:09Z

Agoesman: Created page with "Delete contig dialog."

[[File:DeleteContigDialog.png|Delete contig dialog.]]

GenDBWiki/WebDocumentation/DialogWindows

2011-11-24T14:01:38Z

Agoesman:

__NOTOC__
= GenDB Dialog Windows =

The GenDB Web interface handles a lot of basic functions using dialog windows.
Here, the dialogs are listed and explained.

* [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Window]]
* [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SearchDialog|Search Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/PatScan|PatScan Search]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CircularPlot|Circular Plot]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ReportDialog|Region Report]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|DNA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AA Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ZoomRegionDialog|Region Zoom]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ConfigDialog|Configuration Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|Region Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ExportCDS|CDS Export Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/MultiAnnotator|Multiple Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutation|Mutation Creator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/Virtual2DGel|Virtual 2D Gel Browser]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|Genetic Code Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|Organism and Strain Settings Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/BlastInterface|Blast Interface]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator|Comparative Annotator]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ClusterTool|Gene Cluster Tool]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SequenceViewer|Sequence Viewer]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate|Supporting Observations Editor]]
* [[GenDBWiki/WebDocumentation/DialogWindows/SNP-Detector|SNP Detector]]
* [[GenDBWiki/WebDocumentation/DialogWindows/ToolStatus|Tool Status Dialog]]
* [[GenDBWiki/WebDocumentation/DialogWindows/DeleteContig|Delete Contig Dialog]]

File:DeleteContigDialog.png

2011-11-24T14:00:13Z

Agoesman: Screenshot of the GenDB Delete Contig Dialog

Screenshot of the GenDB Delete Contig Dialog

GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain

2011-11-24T10:01:07Z

Agoesman:

__NOTOC__
This dialog displays the current settings for the attributes "organism", "strain" and "taxonomy ID" of the chosen contig. It allows the user to manage these settings.

In the upper section of the dialog the current settings for the contig will be displayed.

If the user does not know the "taxonomy ID" for an organism, he may use the link to the "NCBI-Taxonomy browser" which is presented within the middle of the dialog.

The lower section of the dialog offers different actions to be performed:

* '''Select from available strains''': The user can select from a drop-down list among all known strains within the current project. The "correspondent organism" will be selected automatically.
* '''Set organism and strain explicitly''': The user can set values for "organism", "strain" and "taxonomy ID" explicitly. This must be done if a new "strain" or "organism" object should be introduced.
* '''Edit settings for organism or strain''': The user can modify existing settings for "organism", "strain" or "taxonomy ID" or add values that have not been specified yet.

By clicking 'OK' the user saves his changes.

[[File:OrganismStrainSelection.png|GenDB Organism and Strain Settings Dialog]]

File:OrganismStrainSelection.png

2011-11-24T09:59:51Z

Agoesman: Screenshot of the GenDB organism and strain selection dialog.

Screenshot of the GenDB organism and strain selection dialog.

GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode

2011-11-24T09:59:12Z

Agoesman:

__NOTOC__
The latest setting for the genetic code of the choosen contig will be displayed. The user can choose a value for the genetic code from a drop down list. Additionally the user may click on the button "Show details for codes" to see in detail of which codons the various supported genetic codes consist of.

[[File:GeneticCodeSelection.png|GenDB Genetic Code Selection Dialog]]

[[File:GeneticCodeDetails.png|GenDB Genetic Code Details]]

File:GeneticCodeDetails.png

2011-11-24T09:58:25Z

Agoesman: Screenshot of the GenDB Genetic Code Detail Viewer

Screenshot of the GenDB Genetic Code Detail Viewer

GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode

2011-11-24T09:57:15Z

Agoesman:

File:GeneticCodeSelection.png

2011-11-24T09:54:41Z

Agoesman: Screenshot of GenDB Genetic Code Selection Dialog

Screenshot of GenDB Genetic Code Selection Dialog