Tutorial

How to use the Web Server
The web server provides all of the options available in the stand-alone version. The instructions for using the web server are provided below.
Application Page
This page is designed to allow to users to submit the protein sequences in FASTA format. These sequences will be analyzed by the Woods software and will segregate these sequences into different functional categories on the basis of their function. Users can submit either the protein sequences from a completed genome where it is assumed that the protein sequences are complete. OR the user can submit the predicted ORFs (nucleotide) file from assembled metagenomic sequences generated using MetaGeneMark. The various parameters which can be specified are highlighted in the following figure.
Sample file: The sample file can be uploaded using the 'Upload Sample File' option.
Results Page Link
After successful upload of the file on the server, a link to retreive the results will appear as shown below. In case of a large sized input which might take a while to process, users can save the link and access their results later.
Results Page
The results will provide the summary of the analysis and links to download the result files as shown below.
HOW TO USE THE STANDALONE PROGRAM
How to install:
The installation instructions are provided on the Download page.
Command line usage for running Woods
./woods <infile> <dataset> <RF model> <method>

infile: Input file containing protein sequences in FASTA format.

dataset: Specify 1 or 2. "1" referes to genomic proteins and "2" refers to metagenomic proteins.

RF Model: Specify the RF model (100) if you wish to use RF model of 100 trees. Default model is of 500 trees

Method: Specify the method of prediction. 'r' for only Random Forest model, Woods is default.

FILE FORMATS AND DESCRIPTION
Input file format The sequences should be in fasta file format.
>r1|info1|info2
SQKLILDKLSFSVPKNSITSILAPNGSGKTTLLKCLLGLLKPLEETEIKACNKDILPLKPYEKAKLI
The ‘info’ in the above example is any information which the user wishes to specify in the annotation line. If the sequences are not in FASTA format or contain any character other than usual amino acid and nucleotide letter codes, the file will not be accepted and an error message will appear.

NOTE : THE UPLOADED FILE NAME SHOULDN'T HAVE ANY BLANK SPACES (for e.g. "sample file" is not allowed)
OUTPUT FILES

Descriptions of the output files.

1. *.Woods.Result: This file provides the output of predictions by Woods in tabular format.

2. RF_pred*: This file provides the output of prediction by Random Forest model alone.