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I have an email database with a couple of thousand members and a twitter account with a couple of thousand followers. Many of them are in both lists for sure.

For the purpose of segmenting the email database, it would be great if I could know who from the email database has a Twitter account.

It's not important to know their Twitter user names or id's, but if that comes as an extra, even better.

Twitter API allows a lot of queries, but I didn't find one that allows search users by email address.

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Couldn't you just give your users an option to enter their Twitter account names? You could give them some kind of incentive to do this. – wssbck Apr 9 '11 at 12:07
@michal-gancarski It's not practical, as open rates for lists go from 15% to 25%. To get to everyone I would need to send 5 to 10 emails focusing on this issue, and defocusing other important issues. Besides it's hard to find an effective and affordable incentive: I might have about 10 thousand positives! – Osvaldo Apr 9 '11 at 16:13

This question on Stack Overflow looks like it would be useful to you:

Twitter API: search people by email

See in particular the link to the 'otherme' method on Google's social graph API:

otherme documentation

NB I've not used this myself and I'm not entirely clear how it would extract Twitter user data based on email if Twitter do not allow API searches based on email but it could be worth exploring.

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