diff options
Diffstat (limited to 'academic/meme-suite/README')
| -rw-r--r-- | academic/meme-suite/README | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/academic/meme-suite/README b/academic/meme-suite/README new file mode 100644 index 0000000000000..f516c7e37141a --- /dev/null +++ b/academic/meme-suite/README @@ -0,0 +1,35 @@ +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 represents motifs as position-dependent scoring matrices. +It consists of programs which allow you to: + +- 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. + +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. + +To cite individual tools, please check the citation page: +http://meme-suite.org/doc/cite.html |