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Select a mulptiple sequence alignment contig file by clicking on 'Browse'. When you've got the file click 'Load SNPF' to load the java program into the browser. Loading the programme without supplying a file will cause an error, You dont want that!
The program needs a java plugin to run so if you do not have one installed already, you will be prompted to download this from the sun microsystems website. Just follow the instructions on installation.
Assuming everything went swimmingly you will see the program Graphical User Interface and depending on which version is running at the time your sequence will be displayed in the sequence box.
There has to be uniniformity in the structure of the data that is supplied to the program.
Firstly the input file must be text so no word documents please, no excel files either.
The sequences must be in FASTA format.
The accession or Sequence I.D MUST be on a separate line.
e.g This is fine >clone101 actagatcgctcgtg---- However, this will not do >clone101acatatcgctcg------ Nor will this >clone101 acatacatacgtc------
If any of these three rules are unenforced the program will not work to specification. I will not be to blame!
Read the user guide for more details
The Applet should run on both Netscape and Internet Explorer browsers, irrespective of the platform ( Windows, MacOs, Solaris, other Unix).
However in testing i have found some problems with Mac9(probably too old OS) and Solaris5.7 machines, havent figured out why yet! Windows works fine!
Whenever i make any changes i will detail them here You need the java applet plugin to run SNPF. However i have rigged it so that you will be automatically redirected to the java plugin download process, just follow the onscreen instructions.
The programme can be graphic intensive on your system so the more memory you got the better! espechially if you are analysing large contigs
I'm still working on the pc version of snpf. This will be made available as son as im satisfied with its performance. Watch this space!You can run a test of the system with this multiple alignment sequence text file.
Simply save it to your harddisk and use it as your input file to load the programme.