Thanks again for responding- I know how annoying these problems are where there are so many posisble issues. But, let me review what does appear to work. I have a list of 1300 regex "rules." I can verify that I get the same results with greta and boost in my annotation program using commands like this: ( rules_annotater is my test program that applies -xrules to -fastas input file and reports results on stdout): 319 $progpath/rules_annotater -boost -doall -fastas onn_fastas -xrules $progpath/prosite_rules > xxxx 321 $progpath/rules_annotater -clean -doall -fastas onn_fastas -xrules $progpath/prosite_rules > yyyy 322 diff xxxx yyyy The diff is clean. I have 1320 rules and the input file contains about 30 text samples, $ more $progpath/prosite_rules | wc 1319 5276 116804 and I get about 2231 hits from the above input data ( "onn_fastas" contains several input strings) $ more xxxx | wc 2231 13406 125169 However, there are very few groups, in fact, ( boost only sees the first word as none of these have white space) $ more $progpath/prosite_rules | grep "(" F[GSTV]PRL([G]|$) >rule|1074|PEPDTIDE Prosite PYROKININ F[IVFY]G[LM]M([G]|$) >rule|1077|PEPDTIDE Prosite TACHYKININ That is why I hope to figure out why the other rule set, containing only 3 rules, has consistent problems. If I thought the build was just plain bad I'd stop everything and fix that first but the only apparent problem is an inability to throw from boost. While I had been testing with different program options, I did just verify that the slight modification to the above command, $ $progpath/rules_annotater -boost -doall -fastas onn_fastas -xrules $progpa th/boost_edit_rulesx will hang when the edit rules file contains things like this: .(...)*?(.)?(H|F|G) >rule|4|Test test Thanks again. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka@hotmail.com Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on marchywka@yahoo.com if no reply here. Thanks. _________________________________________________________________ Peek-a-boo FREE Tricks & Treats for You! http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us