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How do I compare what the user said with an audio recorded sound?

Is there a way to compare 2 audio files, whereby a percentage of difference will be returned? I am using C# VS08, .net framework 3.5.

Edited: difference in the sound(like for eg. Audio 1: "HELP", Audio 2:"HELP ME PLEASE", it will return the difference in percentage between this 2 audio.)

I am currently saving recorded files in wav format, and its bit rate and quality will also be the same as what will be recorded and compared against. I wish to ask if there is a way to compare the sound (not just the binaries) in 2 audio files of the same properties and same format (WAV), and show the percentage difference between the 2 sounds in the 2 audio files.

Help will be greatly appreciated

+1  A: 

I've seen a research paper on the subject recently:

An Industrial-Strength Audio Search Algorithm (PDF)

They compare frequency spectra. The technique is used in a popular iPhone app Shazam.

AnSGri
A: 

Check this: http://social.msdn.microsoft.com/Forums/en-US/vbgeneral/thread/54cef4a3-1c11-4dad-aa13-6ecd8b52cb2a

And if you want to build a system yourself, I think HTK is the best starting point, but you need a solid understanding of Speech recognition as a science to use it perfectly

(By the way: HTK is an open source Speech recognition ToolKit developed @ Cambridge University and now owned by Microsoft)

Sameh Serag