how to calculate elment compostion of fasta protein file using biojava?

Question

[vaibhavt1000]

how to calculate elment compostion of fasta protein file using biojava?

[vaibhavt1000]

I want atomic composition not amino acid composition

[Pierre Lindenbaum]

LMGTFY :

• http://biojava.org/wiki/BioJava:CookBook:Distribution:Composition
• http://biojava.org/wiki/BioJava:CookBook:AAPROP:main#Short_Example_4:_Computing_composition_of_protein_sequence

Answer 1

[Dan D]

I'm not a Java programmer (I use its close cousin C#), but here's the step-by-step that you just need to translate into code:

1. Create a Map<string, int>variable to store the distinct elements and their associated counts.

2. Examine the structure of the AminoAcidComposition.xml file. Each <aminoacid> node has a schema akin to the following:

<aminoacid name="Alanine" shortname="Ala" symbol="A">
        <elements count="3" name="Carbon"/>
        <elements count="1" name="Nitrogen"/>
        <elements count="1" name="Oxygen"/>
        <isotopes count="5" name="Hydrogen"/>
</aminoacid>

3. Use the symbol attribute to identify the correct <aminoacid> node to use for each character in the FASTA sequence. Then cycle through the <elements> nodes, using the name attribute of the node as the key to your Map<string, int> variable, incrementing the value for that key by the value of the countattribute, which you'll probably need to coerce to an int since Java is strongly-typed.