The best tool in my opinion for recording video in Linux is recordMyDesktop. It has good GUI gtk-recordmydesctop and really good performance. You can define its capture area. All calculations runs after capturing process, so it doesn't slow down your computer during that.
Result is written into .ogv file. It can be converted into avi, mp4 without loosing quality with following commands:
ffmpeg -i input.ogv -vcodec libx264 -vpre medium -crf 24 -threads 0 -acodec libfaac output.mp4
ffmpeg -sameq -i input.ogv output.avi
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