We can use the pt-index-usage tool from the Percona Toolkit to get the index analysis. It takes queries from the slow query log, runs the explain plan for each and every query, and identifies the unused indexes. If you have a list of queries, you can save them in slow query format and pass that to the tool. Note that this is only an approximation because the slow query log does not include all the queries:
shell> sudo pt-index-usage slow -u <user> -p<password> /var/lib/mysql/db1-slow.log > unused_indexes
