GLAM / AGLAM 2.1
GLAM is a program for discovering functional motifs shared by a set of nucleotide sequences. Examples of functional motifs include transcription factor binding sites, mRNA splicing control elements, signals for mRNA 3′-cleavage and polyadenylation, and anything else you can dream of. GLAM attempts to find these motifs by obtaining the best possible gapless, multiple alignment of segments of the sequences. The ‘best’ alignment is the one that maximizes the value of a certain formula. At most one segment from each sequence is included in the alignment, and some sequences may be excluded if doing so would improve alignment quality.
AGLAM finds ungapped nucleotide sequence motifs with probabilistic models and sequential (Gibbs) sampling. Its default is double-stranded search, except where noted.
- Linux / SUN Solaris 8 / SGI/IRIX
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Citation for GLAM
Martin C Frith, Ulla Hansen, John L Spouge, Zhiping Weng (2004).
Finding functional sequence elements by multiple local alignment.
Nucleic Acids Research 32(1):189-200.
Ctation for AGLAM
Kim,N-K, Tharakaraman,K, Marino-Ramirez,L, and Spouge,JL
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
BMC Bioinformatics, 2008 Jun 4;9:262.