How to run the applet locally


A very powerful feature of the SeqWord Genome Browser is that it can be run locally on your computer in a web browser. Data is derived from an input sequence using OligoWords, or data exported and saved from the main web database, then results can be simply viewed using a web browser. In this way you can check your newly sequenced genome or any fasta format sequence, such as newly sequenced plasmids or genomic islands.

Requirements
    -    A sequence in fasta or GenBank format 
    -    The two packages from the website
    -    The Java runtime environment with browser plugin (version 5 (1.5) or later)
    -    Python version 2.5

Instructions

From the main SWGB window go to Downloads

Get the packages relevant for your system (here we focus on Windows).

Unzip the packages to separate directories.


1    Obtaining data with OligoWords

Place your genome of interest in fasta (.fst, .fas, .fna) or GenBank (.gbk) format in the OligoWords input directory, or use the provided plasmid pKLC102.fst example already in the directory.

Run OligoWords by double clicking OligoWords1.2.1.exe

The following window should appear:

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Here you can change the list of Tasks to be carried out, and also the length and step of the sliding window.

To change the task list, type 't' and press 'Enter'. New menu will appear that allows you to add or remove tasks from the list. Type 'a' to add a new task and then type 'c' to select task category:

One may select following task categories:

*generalized means that the expected frequency of nucleotides will be normalized by frequencies of constutuent oligonucleotides calculated for the complete genome rather than for a given sliding window (default). 

Next select the scheme of normalization ('n') and the word length ('w'), and type 'a', 'q' and 'q' followed by pressing 'Enter' in three subsequent menus. You'll end up with the first menu (see above). Type 'y' then Enter to start OligoWords. OligoWords will process the fasta/Genbank files in the input directory. The output is plain text files with the extension '.out' in the output directory. The number of output files will be the same as the number of input sequences. 

Note: to ensure reliability of statistical calculations keep in mind that the sliding window length should not be shorter than the following limits. These are set in relation to the maximum word length value.

Word length (bp) Minimum sliding window size (bp)
2 300
3 1200
4 5000
5 18500
6 74000
7 295000

If the word length set for one task requires a larger sliding window, the program will perform calculations as it is set without any warnings, but the resulting values will be statistically unreliable!


2    Viewing output files with the SeqWord Genome Browser locally


To view an output file use the on-line version of the SeqWord Genome Browser or a local version of the applet MhhViewer.html (with associated Java jar file) which is freely available for download. If you use the local applet, open it with your webbrowser and allow the browser to display the applet by accepting the certificate if prompted.

Select File > Open and navigate to the OligoWords output folder to select the results of interest (image below)


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Now you can view and analyse your results just like in the server version of the SeqWord Genome Browser.
Gene names and positions are of course not provided if you only use a fasta sequence, since no annotation exists for the genome with this file type.