Feature encoding

This is the Java implementation for encoding some genome-, proteome- and gene ontology-based features that require data processing.

Here is the list and description of the compiled Java programs:

For genome-based features:

• Nucleotide_composition.java -- calculate 23 nucleotide composition in the coding sequence.
• Codon_usage_CDS.java -- calculate 64 codon usage in the coding sequence.
• Codon_usage_mRNA.java -- calculate 64 codon usage in the mRNA.

For proteome-based features:

• Amino_acid_composition.java -- calculate 37 amino acid composition in the coding sequence.

For gene ontology-based features:

• GO_root_biological_process.java -- map the Gene Ontology term to 29 child term of biological process through the derivation tree.
• GO_root_molecular_function.java -- map the Gene Ontology term to 16 child term of molecular function through the derivation tree.
• GO_root_cellular_component.java -- map the Gene Ontology term to 21 child term of cellular component through the derivation tree.

Instruction

Our codes require support from Java Platform and Standard Edition Development Kit (JDK).

They are well supported in Linux or mac OS.

There are only five simple steps to use our codes:

• Step 1: install a JDK (version 8+) environment on your computer;
• Step 2: download Compiled_code.zip and uncompress it;
• Step 3: add your nucleotide, protein sequences or gene ontology profiles in the example files (e.g., /compiled_code/data/Protein_example.txt);
• Step 4: ues 'Terminal' to the directory of 'Compiled_code';
• Step 5: use 'java [program_name]' to encode features for your sequences or gene ontology profiles (e.g., java Nucleotide_composition).

Input and output examples

The example input files are placed at /HIVPRE/data/ while outputs for them can be found at /HIVPRE/Example_output/.

Here is the list and description for the input examples:

• DNA_CDs_example.txt -- 3 coding sequences in FASTA format.
• mRNA_example.txt -- 3 mRNA sequences in FASTA format.
• Protein_example.txt -- 3 protein sequences in FASTA format.
• Gene_Ontology_example.txt -- 6 genes ontology annotaion data.

Web server

Our web server for the HIVPRE project is accessible at: http://hivpre.cvr.gla.ac.uk/.

Citation

Chai H, Gu Q, Hughes J, Robertson DL (2022) In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Comput Biol 18(2): e1009720. https://doi.org/10.1371/journal.pcbi.1009720