First of all, I have no problem naming my sequences with _seq. I just wanted to know why PEAR automatically appended it. It would seem to me that the naturally way of doing it would be to call nextID('publication_seq') if that is what the name rather than nextID('publication'). Espcially being concerned with code readability. People reading the code seeing 'publication' but then seeing the name 'publication_seq' in the database would most likely be very confused.
Second of all, just in case anyone else wonders, it is a configural option in PEAR of how you want to your sequences named. Just use $dbh->setOption('seqname_format' , '%s'); to keep if from appending '_seq'.
Thanks a lot for your critiscm. If you don't have a helpful answer or explanation maybe you shouldn't reply at all. Just saying "your doing it wrong" never helped anybody. Especially when I was doing it correctly, I just didn't realize there where configuration options. And apparently you didn't either so just stop pretending like you know everything.