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diff --git a/academic/meme-suite/README b/academic/meme-suite/README index f516c7e37141a..b48cdaf9f765c 100644 --- a/academic/meme-suite/README +++ b/academic/meme-suite/README @@ -1,35 +1,31 @@ The MEME suite: motif based sequence analysis tools -The MEME suite provides tools for discovering and using protein and -DNA sequence motifs. A motif is a pattern of nucleotides or amino acids -that appears repeatedly in a group of related DNA or protein sequences. +The MEME Suite allows the biologist to discover novel motifs in +collections of unaligned nucleotide or protein sequences, and to perform +a wide variety of other motif-based analyses. The Suite supports motif- +based analysis of DNA, RNA and protein sequences. It provides motif +discovery algorithms using both probabilistic (MEME) and discrete models +(MEME), which have complementary strengths. It also allows discovery of +motifs with arbitrary insertions and deletions (GLAM2). In addition to +motif discovery, the MEME Suite provides tools for scanning sequences +for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters +of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding +preferred spacings between motifs (SpaMo), predicting the biological +roles of motifs (GOMo), measuring the positional enrichment of sequences +for known motifs (CentriMo), and analyzing ChIP-seq and other large +datasets (MEME-ChIP). -The MEME suite represents motifs as position-dependent scoring matrices. -It consists of programs which allow you to: +Check README.TESTS for runing the recommended tests on the compiled +executables. Here, the tests *FAIL* on a 32bit system! -- meme - discovery of motifs shared by a group of sequences -- mast - search of databases for sequences containing these motifs -- tomtom - searching databases of motifs for similar motifs -- gomo - finding Gene Ontology terms linked to the motifs -- glam2 - discovery of gapped motifs -- glam2scan - scanning sequences with gapped motifs -- fimo - scanning sequences with motifs -- mcast - finding motif clusters -- meme-chip - analysis of large DNA datasets like ChIPseq output -- spamo - finding motif complexes by analysing motif spacing -- dreme - discovery of short regular expression motifs - -Note: building on a 32bit architecture fails at the 'make test' step -(check script). If the step is disabled, the suite builds, however it -may or may NOT work properly. Therefore, 32bit is set as 'UNTESTED'. -The 'make test' step will also fail if you don't build in a proper root -environment. +Check README.DATABASES for more info or if you want to install +meme-suite without the databases present at build time. To cite the full MEME suite: -Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, -Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, -William S. Noble, "MEME SUITE: tools for motif discovery and searching", -Nucleic Acids Research, 37:W202-W208, 2009. +Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles +E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, +"MEME SUITE: tools for motif discovery and searching", Nucleic Acids +Research, 37:W202-W208, 2009. To cite individual tools, please check the citation page: http://meme-suite.org/doc/cite.html |