Motif Properties

Description

The Motif_Properties format will output a table with one motif on each row and with columns containing information about different motif properties chosen by the user. In MotifLab v2.0+ this format can also be used to import motif collections.

Example of properties output with the format string "ID,Short name,Classification,Consensus" (with header)

#ID Short name Classification Consensus M00006 V$MEF2_01 4.4.1.1 CTCTAAAAATAACyCy M00005 V$AP4_01 1.3.1.4 wGAryCAGCTGyGGnCnk M00008 V$SP1_01 2.3.1.0 GGGGCGGGGT M00007 V$ELK1_01 3.5.2.0 nAAACmGGAAGTnCGT M00002 V$E47_01 1.2.1.0 vsnGCAGGTGknCnn M00001 V$MYOD_01 1.2.2.0 srACAGGTGkyG M00004 V$CMYB_01 3.5.1.1 nCnrnnGrCnGTTGGkGG M00003 V$VMYB_01 3.5.1.1 AATAACGGnA

Arguments

Name	Description
Format	This parameter specifies which motif properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive! Standard motif properties include: ID Short name Long name Consensus Size IC-content GC-content Factors Classification Class name Quality Part Alternatives Interactions Organisms Expression Matrix When importing motifs from an existing file, the `format` parameter should list the properties in the order they appear in the file. If the file contains more properties than you want to import, you are allowed to specify only a subset. For example, if the file has the following five properties ID, Short name, Consensus, Quality and Organisms (in that order), and you only want to import the first three, you can just set the format parameter to "`ID, Short name, Consensus`" and the remaining properties will simply be ignored. You can also skip properties in the middle of the list by replacing the property name with an asterisk. To import only the properties ID, Consensus and Organism from the mentioned file (i.e. only columns 1,3 and 5), set the `format` parameter to "`ID,,Consensus,,Organisms`". If the file contains a "header" in the first line (starting with # and describing all the properties), you can use this header rather than naming the properties explicitly by setting the `format` parameter to a single asterisk (`*`). Note that the ID property must always be included or MotifLab will complain.
Separator	This parameter specifies how to separate the motif properties on each line in the output. The character chosen as the separator will replace the commas in the format string above. Valid options for the separator are "TAB" (default), "Comma", "Semicolon", "Colon" and "Vertical bar".
List-separator	Some motif properties may be represented by lists (e.g. binding factors and alternative motif models). The "List-separator" parameter specifies how to separate the entries in such lists. Valid options are "Comma" (default), "TAB", "Semicolon", "Colon" and "Vertical bar". Note that this separator should be different from the separator used to separate the motif properties that are output.
Header	If this option is selected, a header line starting with # will be included at the beginning of the output. The header line describes which motif properties are included.

Name

Description

Format

This parameter specifies which motif properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive!

Standard motif properties include:

ID
Short name
Long name
Consensus
Size
IC-content
GC-content
Factors
Classification
Class name
Quality
Part
Alternatives
Interactions
Organisms
Expression
Matrix

When importing motifs from an existing file, the format parameter should list the properties in the order they appear in the file. If the file contains more properties than you want to import, you are allowed to specify only a subset. For example, if the file has the following five properties ID, Short name, Consensus, Quality and Organisms (in that order), and you only want to import the first three, you can just set the format parameter to "ID, Short name, Consensus" and the remaining properties will simply be ignored. You can also skip properties in the middle of the list by replacing the property name with an asterisk. To import only the properties ID, Consensus and Organism from the mentioned file (i.e. only columns 1,3 and 5), set the format parameter to "ID,*,Consensus,*,Organisms". If the file contains a "header" in the first line (starting with # and describing all the properties), you can use this header rather than naming the properties explicitly by setting the format parameter to a single asterisk (*). Note that the ID property must always be included or MotifLab will complain.

Separator

This parameter specifies how to separate the motif properties on each line in the output. The character chosen as the separator will replace the commas in the format string above. Valid options for the separator are "TAB" (default), "Comma", "Semicolon", "Colon" and "Vertical bar".

List-separator

Some motif properties may be represented by lists (e.g. binding factors and alternative motif models). The "List-separator" parameter specifies how to separate the entries in such lists. Valid options are "Comma" (default), "TAB", "Semicolon", "Colon" and "Vertical bar". Note that this separator should be different from the separator used to separate the motif properties that are output.

Header

If this option is selected, a header line starting with # will be included at the beginning of the output. The header line describes which motif properties are included.

output

HTML_MotifTable

Module_Properties

Sequence_Properties

Properties