What does this mean? "PUB.PUBLSEQ LIKE '%%%%%J'"
and what is the difference from this? "PUB.PUBLSEQ LIKE '%J'"
You can use only one "%" that means any and many times. You don't need to repeat it. It is not wrong but looks weird.
For optimizing your query:
1) take an explain plan for your query and focus on high costs and full table accesses.
2) using functions on where clause prevents index usage, if function usage is dispensable get rid of it.
3) adding indexes on columns used for joins may help, but it should be analyzed. Query optimization and sql tuning does not mean adding index on all join columns. A dba may help you on index analysis.