release_notes.html
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<!---#### $Id: release_notes.html 1342 2006-09-21 20:44:23Z tbailey $#### $Log$## Revision 1.15 2006/03/07 23:30:20 nadya## merge branches v3_5_1 and v3_5_2 back to the trunk#### Revision 1.14.6.2 2006/03/01 19:35:21 nadya## add changes and fixes for v 3.5.2#### Revision 1.14.6.1 2006/02/22 20:49:02 nadya## enabling styling with js and css#### Revision 1.14 2005/12/16 23:44:10 nadya## add note about mac support. Rm bad entries form previously committed version#### Revision 1.13 2005/12/16 05:14:02 tbailey## Added CYGWIN support.#### Revision 1.12 2005/12/15 21:13:53 nadya## initial revision.## This file should go on the web download site.#### Revision 1.11 2005/12/01 03:54:53 tbailey## Add JASPAR search button to New Features section for next release.#### Revision 1.10 2005/10/13 21:14:53 nadya## add bug fixes for Globals.pm and meme-explanation.html#### Revision 1.9 2005/10/08 00:35:24 nadya## add notes for v.3.5.1## restore desription of bug in v3.5.0 (binary and scripts names)#### Revision 1.8 2005/09/28 21:00:23 nadya## rm usage changes section from v 3.5.0. Update layout throughout.#### Revision 1.6 2005/09/27 00:51:04 nadya## add usage changes (meme vs. meme.csh)#### Revision 1.5 2005/09/21 21:34:50 nadya## add comments on improvements/changes#### Revision 1.4 2005/09/19 06:08:03 wilfred## fixed typos and other grammar issues#### Revision 1.3 2005/09/16 04:54:51 wilfred## updated release notes#### Revision 1.2 2005/09/16 01:23:42 wilfred## updated release note for version 3.5#### Revision 1.1.1.1 2005/07/31 20:19:18 nadya## Importing from meme-3.0.14, and adding configure/make####---><HTML><HEAD><TITLE>MEME - Release Notes</TITLE><script src="template-css.js" type="text/javascript"></script></HEAD><body class="body"><table class="maintable"><script src="template-header.js" type="text/javascript"></script> <center><H2> MEME System Release Notes </H2></center><HR><P><B>MEME version 3.5.4 -- September 21, 2006 </B><UL> <LI><B> New Features and Enhancements </B> <UL> <LI>Changed the MAST -hit_list behavior to print ONLY a list of the non-overlapping significant motif matches in each sequence in a machine-readable format. (More complete documentation is given in the MAST "usage" message. Type "mast" on the UNIX command line to see the usage message.) An example of the (complete) output of MAST using the -hit_list switch is: <pre> # All non-overlapping hits in all sequences with E-values <= 10. # sequence_name motif hit_start hit_end hit_p-value ara +2 2 16 6.55e-08 ompa +2 5 19 2.74e-07 ce1cg -2 8 22 2.12e-06 bglr1 +2 1 15 1.48e-05 cya -2 19 33 6.91e-05 ilv -2 6 20 7.61e-05 malk +2 37 51 8.37e-05 gale +2 5 19 8.37e-05 # mast tests/meme.crp0.oops tests/crp0.s -stdout -hit_list -m 2 </pre> <LI>New "regular expression" section added to each MEME motif. </UL> <LI><B>Bug fixes </B> <UL> <LI>Fixed printing of command name in MAST results. <LI>Fixed the handling of the "View FASTA", "View RAW" and "View motif summary" buttons on the MEME form. <LI>Improved documentation of the "Motif Summary" section of MEME output. <LI>Fixed bug that prevented having multiple MEME and MAST servers running on a single host by different users. Each server is distinguished by the socket number it listens on. </UL> <LI><B>Known Issues </B> <UL> <LI>The "MetaMEME" button on the top of MEME results page is still not functional. Users are advised to go to the MetaMEME web site and submit manually at this time. <LI>MAST: Uploaded file names containg quotation marks may cause the search to fail. <LI>MAST: Uploaded sequences in DOS/Windows format may cause the search to fail. </UL></UL><HR><P><B>MEME version 3.5.3 -- April 20, 2006</B><UL> <LI><B> New Features and Enhancements </B> <UL> <LI>The capability to search three JASPAR databases of DNA motifs for matches to a MEME-discovered motif has been added to the MEME output form. Pressing the 'COMPARE PSPM' button on the results form of a MEME search of DNA sequences will submit the selected motif PSPM to the JASPAR 'Compare' server. This will allow you to determine if your motif is similar to any known motifs contained in one of the three JASPAR motif databases. </UL> <LI><B>Bug fixes </B> <UL> <LI>The "MAST" button on the top of MEME results page now automatically loads the motifs from the MEME results for MAST search. A user only needs to choose the database (uploaded or server side) to search against. </UL> <LI><B>Known Issues </B></UL><HR><P><B>MEME version 3.5.2 -- March 1, 2006</B><UL> <LI><B> New Features and Enhancements </B> <UL> <LI>Newly designed web insterface using javascript and css styling. <LI>Add support for Macos X server startup. <LI>Add meme-install.html with detailed explanation of installation procedures. </UL> <LI><B>Bug fixes </B> <UL> <LI>In "configure" remove check dependency on parallele condition when creating server executables. <LI>Path to images/ in cgi scripts. <LI>Description syntax in linux startup script meme.linux. <LI>Provide fix for a cygwin's new line representation when searching strings. <LI>Bug in e_step (oops.c) <LI>Bug caused by typo "MEME_BINbin" <LI>Remove use of min() in meme.pl <LI>Remove obsolete argument sample_prob from subseq7() <LI>Remove OS-dependent declarations of accept(), bind(), connect(), socket(), listen(), htons(). They are defined in system header files. </UL></UL><HR><P><B>MEME version 3.5.1 -- December 15, 2005 </B><UL> <LI><B>Bug fixes </B> <UL> <LI>Revert binary and scripts names to what they used to be in version prior to 3.5.0. The binary executables have an extension ".bin", and the shell scripts have their extension ".csh" removed. This allows to keep compatibility with earlier versions. <LI>Change startup scripts to start servers as a user specified during configuration. If none were specified, then the uid of the user who runs configure will be used. <LI>Always install files in etc/. <LI>Always install Globals.pm in lib/perl/. <LI>Move meme-explanation.html from web/html/ to etc/. This allows to run scripts that do conversion to html when web site is not installed. </UL> <LI><B>Enhancements</B> <UL> <LI> Added support for Macos X (serial verison only, without server) <LI> Users can now compare DNA motifs to the motifs in the JASPAR database of transcription factor binding site motifs. A button is provided in the PSPM section of each DNA motif on the MEME output form for this purpose. Clicking on the "Compare PSPM x to known motifs in JASPAR database" sends the motif to the JASPAR website, which returns any similar motifs that are found. <LI>Add meme_config.csh file that is used automatically by csh scripts to set needed environment variables. <LI>Move job.out file (created when SGE scheduler is used) to LOGS/ <LI>Add '--with-serial' option to 'configure.ac' for compiling only serial version <LI>Disable installlation of web by default. To install use --with-web configure option. <LI>Lower prerequisite verison for autoconf to 2.53, and add missing functions in m4/. Add check for autoconf verison in bootstrap, and use m4 functions when needed. <LI>Change option '--with-mpi' to '--with-mpidir' </UL></UL><HR><P><B>MEME version 3.5.0 -- September 15, 2005 </B><P>This is the <B>12th year of MEME development</B>. The current anniversary maintenance release for MEME contains a number of improvements to the installation and configuration of MEME/MAST servers and clients. Thanks to Nadya Williams of SDSC/NBCR for this work.<UL> <LI><B>Refactoring of installation and configuration</B> <UL> <LI>Restructure source directory tree to ease configuration. <LI>Highly simplified and optimized installation and configuration for MEME and MAST servers and clients using GNU autoconf/automake tools. <LI>Multiple configuration options available via arguments to "configure". <LI>Default installation of MEME, MAST server and clients, as well as the web site. <LI>Separate installatiion of server, client or web site if desired. <LI>Create a small test suite for 'make test'. <LI>Implement procedures for standard 'configure', 'make', 'make test', and 'make install'. <LI>Create scripts to run MEME/MAST servers as services, and automatically restarted them when physical host server reboots. Currenly, Linux and SunOS are supported. <LI>Simplified start of the servers with 'start-mast' and 'start-meme' scripts. <LI>Encapsulate site-specific variables in Globals.pm for perl scripts and in meme_config for sh scripts. <LI>Add csh and sh configuration scripts to set working environment. <LI>Availability as a Rocks Roll for integration with <a href="http://www.rocksclusters.org">Rocks based cluster system</a>. </UL> <LI><B>Enhancements</B> <UL> <LI>Sent MEME/MAST search results via an email as attachments, rather than inlined in the message body. This allows the MEME output to be saved properly for subsequent use with MetaMEME. It also reduces the chance of the output being modified by email filters. <LI>Check email addresses for entry accuracy using javascript. Thanks to Chris Misleh of NBCR for this feature. <LI>Check email addresses for valid domain names. <LI>Create new 'runtests' script to run all test suites. Simplify parsing of the output. <LI>Update FAQ(s) for MEME and MAST. <LI>Separate web-related files by type (html, cgi or image) and create a dir structure to support it. This simplifies web maintenace. <LI>Add examples of database and motif sequences files. </UL> <LI><B>Known Issues</B> <UL> <LI>The new meme and mast are binary executables, not shell scripts as they used to be. When run with the appropriate arguments, they produce text (non-html) output. To get the "old" behavior of meme and mast with the html output, use meme.csh and mast.csh (without -text option). The following table gives new vs. old usage comparison. <pre> old new meme myfile -dna -text > meme.res meme myfile -dna > meme.res # output will be a text file meme myfile -dna > meme.res meme.csh myfile -dna > meme.res # output will be an html file mast meme.res mast.csh meme.res # output will be an html file</pre> </UL> <LI><B>Support Team Members</B> Wilfred W. Li, Ph.D., Nadya Williams, M.S., Chris Misleh, and Tim Bailey, Ph.D.</UL><HR><P><B>MEME version 3.0.14 -- July, 2005 </B><P><UL> <LI><B>Bug Fixes</B> <UL> <LI>an array out of bound error when MEME is run in parallel mode using certain DNA sequences with the "look for palindromes only" option enabled. Thanks to Tim Kaiser of SDSC/NBCR for the bug fix. </UL> <LI><B>User Support</B> <UL> <LI>all user questions are directed to our support team meme@nbcr.net. </UL></UL>⌨️ 快捷键说明
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