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Created page with '=== How can I compute PROFEAT properties via APIs? === BioJava provides a set of APIs to generate PROFEAT properties.<br> PROFEAT generate properties of a protein sequence base…'
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‎_wikis/BioJava:CookBook:AAPROP:profeat.md‎

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---
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title: BioJava:CookBook:AAPROP:profeat
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---
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### How can I compute PROFEAT properties via APIs?
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BioJava provides a set of APIs to generate PROFEAT properties.
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PROFEAT generate properties of a protein sequence based on its
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converted attributes.
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\* The seven different attributes are
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`* Hydrophobicity (Polar, Neutral, Hydrophobicity)`
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` * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)`
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` * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)`
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` * Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)`
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` * Charge (Positive, Neutral, Negative)`
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` * Secondary structure (Helix, Strand, Coil)`
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` * Solvent accessibility (Buried, Exposed, Intermediate)`
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Please see
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[PROFEAT](http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract)
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for more information about these properties.
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The class providing the core functionality for this is the
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IProfeatProperties class.
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Short Example 1: Computing composition of the various grouping for all seven attributes
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---------------------------------------------------------------------------------------
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<java> String sequence =
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"QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE, Map<GROUPING, Double>\> attribute2Grouping2Double =
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ProfeatProperties.getComposition(sequence); for(ATTRIBUTE
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a:attribute2Grouping2Double.keySet()){
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`   System.out.println("=======" + a + "=======");`
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`   System.out.println("GROUP1 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP1));`
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`   System.out.println("GROUP2 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP2));`
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`   System.out.println("GROUP3 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP3));`
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`   System.out.println();`
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} </java>
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Short Example 2: Computing the number of transition between various grouping for all seven attribute with respect to the length of sequence
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-------------------------------------------------------------------------------------------------------------------------------------------
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<java> String sequence =
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"QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE, Map<TRANSITION, Double>\> attribute2Transition2Double =
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ProfeatProperties.getTransition(sequence); for(ATTRIBUTE
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a:attribute2Transition2Double.keySet()){
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`   System.out.println("=======" + a + "=======");`
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`   System.out.println("1<=>1 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_11));`
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`   System.out.println("2<=>2 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_22));`
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`   System.out.println("3<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_33));`
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`   System.out.println("1<=>2 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_12));`
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`   System.out.println("1<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_13));`
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`   System.out.println("2<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_23));`
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`   System.out.println();`
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} </java>
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(See also: [How to define the XML files to customize mass of Amino Acids
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in the computation of Molecular
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Weight?](BioJava:CookBook:AAPROP:xmlfiles "wikilink"))
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Short Example 3: Computing the position with respect to the sequence where the given distribution of the grouping can be found
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------------------------------------------------------------------------------------------------------------------------------
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<java> String[] sequences = new String[3]; String sequence =
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"QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>\>\>
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attribute2Grouping2Distribution2Double =
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ProfeatProperties.getDistributionPosition(sequence); for(ATTRIBUTE
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a:attribute2Grouping2Distribution2Double.keySet()){
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`   System.out.println("=======" + a + "=======");`
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`   System.out.println("GROUP1 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP1));`
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`   System.out.println("GROUP2 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP2));`
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`   System.out.println("GROUP3 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP3));`
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} </java>

‎_wikis/BioJava:CookBook:AAPROP:profeat.mediawiki‎

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=== How can I compute PROFEAT properties via APIs? ===
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BioJava provides a set of APIs to generate PROFEAT properties.<br>
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PROFEAT generate properties of a protein sequence based on its converted attributes.<br/>
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* The seven different attributes are<p/>
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* Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
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* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
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* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
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* Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)<br/>
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* Charge (Positive, Neutral, Negative)<br/>
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* Secondary structure (Helix, Strand, Coil)<br/>
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* Solvent accessibility (Buried, Exposed, Intermediate)<br/>
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Please see [http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract PROFEAT] for more information about these properties.<br>
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The class providing the core functionality for this is the IProfeatProperties class.<br>
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==Short Example 1: Computing composition of the various grouping for all seven attributes ==
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<java>
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE, Map<GROUPING, Double>> attribute2Grouping2Double = ProfeatProperties.getComposition(sequence);
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for(ATTRIBUTE a:attribute2Grouping2Double.keySet()){
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System.out.println("=======" + a + "=======");
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System.out.println("GROUP1 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP1));
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System.out.println("GROUP2 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP2));
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System.out.println("GROUP3 = " + attribute2Grouping2Double.get(a).get(GROUPING.GROUP3));
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System.out.println();
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}
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</java>
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==Short Example 2: Computing the number of transition between various grouping for all seven attribute with respect to the length of sequence==
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<java>
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE, Map<TRANSITION, Double>> attribute2Transition2Double = ProfeatProperties.getTransition(sequence);
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for(ATTRIBUTE a:attribute2Transition2Double.keySet()){
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System.out.println("=======" + a + "=======");
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System.out.println("1<=>1 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_11));
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System.out.println("2<=>2 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_22));
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System.out.println("3<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_33));
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System.out.println("1<=>2 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_12));
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System.out.println("1<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_13));
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System.out.println("2<=>3 = " + attribute2Transition2Double.get(a).get(TRANSITION.BETWEEN_23));
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System.out.println();
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}
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</java>
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(See also: [[BioJava:CookBook:AAPROP:xmlfiles|How to define the XML files to customize mass of Amino Acids in the computation of Molecular Weight?]])
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==Short Example 3: Computing the position with respect to the sequence where the given distribution of the grouping can be found==
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<java>
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String[] sequences = new String[3];
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String sequence = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE";
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Map<ATTRIBUTE , Map<GROUPING, Map<DISTRIBUTION, Double>>> attribute2Grouping2Distribution2Double = ProfeatProperties.getDistributionPosition(sequence);
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for(ATTRIBUTE a:attribute2Grouping2Distribution2Double.keySet()){
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System.out.println("=======" + a + "=======");
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System.out.println("GROUP1 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP1));
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System.out.println("GROUP2 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP2));
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System.out.println("GROUP3 = " + attribute2Grouping2Distribution2Double.get(a).get(GROUPING.GROUP3));
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}
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</java>

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