Changes Files Description ----- ----------- configure, configure.ac Fixed compiler flags in configure to allow programs to access files larger than 4GB. etc/tomtom-to-html.xsl Added alternate name to Tomtom summary. scripts/meme2meme.pl Fixed a bug in meme2meme.pl related to parsing meme files without logodds sections. scripts/runcheck_p.in Removed duplicate MAST tests from parallel checks (MAST is not parallel). src/background.c Fixed a bug with higher order background when sequences contain Xs. src/hash_alph.h Added new amino acid ambiguity codes: J, O, U. src/meme.c Tweaked output. src/pmp_bf.c Added better usage message to pmp_bf. src/tomtom.c Changed Tomtom to allow different databases to share the same motif names so they don't get excluded. .../tomtom_request.pl Changed perl print from "$fh->print(text);" to "print $fh text;" to work with older versions of Perl. Files changed in patch: configure configure.ac etc/tomtom-to-html.xsl scripts/meme2meme.pl scripts/runcheck_p.in src/background.c src/hash_alph.h src/meme.c src/pmp_bf.c src/tomtom.c website/cgi-bin/tomtom_request.pl Installing the patch: 1) Change into the root meme_4.5.0 distribution directory 2) Apply the patch by running: patch -p1 -i PATH_TO_PATCH/meme_4.5.0.patch_1 3.1) If this is a new install run: ./configure [subsitute your normal arguments here] (also don't forget to install the databases) 3.2) Or if you are updating an existing installation then run: ./config.status --recheck; ./config.status 4) Update timestamps on files by running the following: touch aclocal.m4; touch configure; touch config.status; touch config.h.in; touch Makefile.in 5) Rebuild everything by running: make clean; make 6) Install by running: make install If run on split server (separate Apache and Tomcat servers) this patch needs to be applied to both sides.