Disavowing Links: Over-optimized Anchor Text
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If a site has been effected by Penguin, and the main issue is over-optimized anchor text. Would the disavow file take care of this?
If there is a no-follow added to the link when Google next crawls the site, wouldn't you still have the optimized anchor text in your profile?
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How do you know the main issue is over-optimized anchor text? Did you get a manual action notification in GWT or is this effect your assumption? This would be an important distinction because you'd get some good info from the GWT team about what happened to your site. Some sites take a temporary hit after new algorithm updates, so if this just happened I'd give it a little time before making drastic changes to your site.
It's unclear whether it's your site that's hosting the links or if other site(s) are linking to yours. Follow Googles guidelines about linking https://support.google.com/webmasters/answer/2648487?hl=en and read up on how and why to disavow backlinks here https://support.google.com/webmasters/answer/2648487?hl=en. Being honest to yourself is the best policy here, so if you're taking or paying money for these links, you or your associates should use the nofollow attribute according to Google's guidelines. You can learn more about anchor text here on MOZ http://moz.com/learn/seo/anchor-text. It's believed that links with the nofollow attribute won't pass PageRank, so the anchor text of such links won't hurt or help with search engines but may be valuable to your readers. More about how to use the nofollow attribute here https://support.google.com/webmasters/answer/96569?hl=en.
Now if you actually got notified of a manual action, then you'll need to submit a reconsideration request in GWT. We don't have enough information here on how Google will deal with your site on the next crawl, but I would recommend a consistent, site-wide approach to SEO rather than just changing a few links you think might be hurting you.
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No manual action. I have seen some fluctuation in rankings, and I am trying to figure out if it is Penguin related.
Thanks for the help.