Changes (in chronological order) Files Description ----- ----------- scripts/meme2meme.pl.in Fixed a bug which was interfering with reading meme text format protein motifs. scripts/MotifsUtils.pm Subroutine intern_to_iupac changed to not use ambiguous characters when describing protein motifs (was resulting in all X). src/mast2text.c Fixed a bug where large residue counts were causing integer overflow. etc/tomtom-to-html.xsl Changed the summary section so the list of motifs is easier to read when there are a lot of motifs. --various html-- Fixed a typo that doubled up the '>' after a script tag. The typo had been copied to many files. etc/fimo-to-wiggle.xsl Fixed error in Wiggle format: Ensmble requires variableStep rather than variablestep (note the capitalisation). scripts/meme-chip.pl.in Changed tar creation to tar the parent directory and avoid a tar-bomb. scripts/meme-chip.pl.in MAST and AMA were creating huge files and most people won't need them so they now only run on request. src/mast.c MAST was failing occasionally on large (> 4Gb) databases due to caching file positions in 32 bit integers which overflowed scripts/tamo2meme.pl.in Fixed handling of identical names. src/readseq.c, src/ureadseq.c & src/ureadseq.h Fix to overflow in sequence counter when more than 32767 sequences. scripts/MemeWebUtils.pm.in Avoid calling readseq when file is already in fasta format. scripts/MemeWebUtils.pm.in Improved help/error messages for get_sequence_data. website/cgi-bin/ (meme|tomtom)_request.pl Replaced call to convert (Image Magick) with gs (Ghostscript). Eventually we won't need Image Magick... etc/motif_logo.js Fixed handling of tab characters at end of last line of the pspm. Now they are trimmed properly. -- various perl scripts-- Improved tempfile usage. Installing the patch: 1) Change into the root meme_4.6.1 distribution directory 2) Apply the patch by running: patch -p1 -i PATH_TO_PATCH/meme_4.6.1.patch_1 3) Make the install files: make 3) Install by running: make install If run on split server (separate Apache and Tomcat servers) this patch needs to be applied to both sides.