Similar to Doctrine_Core::ATTR_IDXNAME_FORMAT, Doctrine_Core::ATTR_SEQNAME_FORMAT can be used for changing the naming convention of sequences. By default Doctrine uses the format [name]_seq, hence creating a new sequence with the name of mysequence will lead into creation of sequence called mysequence_seq.
You can change the sequence naming convention with the following code:
// bootstrap.php
// ...
$manager->setAttribute(Doctrine_Core::ATTR_SEQNAME_FORMAT, '%s_sequence');