ConDens


  1. Installation/Program Structure
  2. ConDens Predictor
  3. ConDens Browser
  4. Structure of Alignment Input
  5. Structure of Data Output
  6. Regular Expressions in ConDens
  7. Modifying Default Program Settings
Adding new presets

ConDens Predictor automatically looks for pre-available proteomes and alignments sets in the local directory. A new proteome or alignment set can be added by placing the relevant data in a new folder under data/proteins or data/msa, respectively. This new folder should contain a file called info.xml that has the following structure:

Sample info.xml file


Figure 1: The program can be set to automatically load custom lists of proteins and multiple sequence alignments

Figure 1: The program can be set to automatically load custom lists of proteins and multiple sequence alignments

<!-- Root node -->
<settings>

<!-- An internal node that indicates whether this describes a proteome or an alignment set. In this example, this file is for a proteome so this node is called "proteins". If this file is for an alignment set, then it should be called "msa" instead. -->
<proteins>

<!-- Name of this new dataset -->
<name>My list of proteins</name>

<!-- Description of this dataset. -->
<description>Proteins that my favourite undergraduate slave pulled out yesterday from a Co-IP experiment.</description>

<!-- File path that points to the location of the dataset file, which is of the same input format as what's expected for the ConDens predictor program. This file path must be defined relative to info.xml's parent directory. In this example, the file is located in the same directory as info.xml. -->
<path>gene_list.txt</path>

</proteins>

</settings>

Default Settings of ConDens Predictor

It can be very bothersome having to re-pick input parameters and type up the same motif regular expressions over and over again when one opens the program each time. To reduce this annoyance factor, preferred input settings of this program can be specified in data/default.xml. This file takes the exact same form as the command-line XML input of the program. See here. Default Settings of ConDens Browser

The default settings of ConDens Browser can be defined in data/default_viewer_settings.xml. This file has almost the exact same structure as data/default.xml but with fewer nodes:

Sample default_viewer_settings.xml

<!-- Root node -->
<settings>

<!-- The number of rows to display on the Data Window. This is defaulted to 2000. Setting this to a larger number can make large tables easier to scroll through at the cost of computational efficiency. -->
<param rowlimit="2000" />

<!-- The folder of the default dataset to load. This dataset is expected to be the output data of ConDens predictor. -->
<output path="yeast_output_data" />

<!-- The set of sequence alignment to use where "path" indicates the file path to the alignment_mapping file. This file path is relative to the location of data/default_viewer_settings.xml-->
<msa path="msa/my_alignments/mapping_file.tab" />

<!-- A list of motifs with consensus sequences as regular expressions. -->
<consensuses>

<!-- A motif. "name" denotes the name of the motif and "regex" denotes its regular expression -->
<consensus name="Cdk" regex="(?<r>[ST])P" />
<consensus name="Mec1" regex="(?<r>[ST])Q" />
<consensus name="Prk1" regex="[LIVM]XXXX(?<r>T)G" />
<consensus name="Ipl1" regex="[RK]X(?<r>[ST])[LIV]" />
<consensus name="PKA" regex="R[RK]X(?<r>S)" />
<consensus name="CKII" regex="(?<r>[ST])[DE]X[DE]" />
<consensus name="Ime2" regex="RPX(?<r>[ST])" />

</consensuses>

</settings>

Changing the Library of Motifs

The repository of short linear motifs provided are not very comprehensive. Should there be a need to make changes to it, the relevant file to modify is data/consensus_library.xml, which stores a list of motifs and their information. This file has the following structure:

Sample consensus_library.xml

<!-- Root nodes -->
<library><consensuses>

<!-- Entry of a motif with its name as attribute -->
<consensus name="Cdk">

<!-- Regular expression of motif -->
<regex>[ST]P</regex>

<!-- A reference associated with the definition of this motif -->
<ref>

<!-- Textual description of reference, such as bibliography entry. HTML formating is supported -->
<text>Hunter T, Plowman GD: <b>The protein kinases of budding yeast: six score and more</b>. <i>Trends Biochem. Sci </i>1997, <b>22</b>:18-22. </text>

<!-- Any ID's or URL associated with this reference. Only PMID and URL are supported for now. -->
<id type="PMID">9020587</id>

<id type="URL">http://www.ncbi.nlm.nih.gov/pubmed?term=9020587</id>

</ref>

<!-- More references -->
</ref>
...
</ref>

</consensus>

<!-- More motifs -->
<consensus>
...
</consensus>

</consensuses></library>