All calculations were done using the Biopython motif package and custom python scripts [ 71, 72].
The peak-motif package (Thomas-Chollier et al. 2011) of RSAT was used for evaluating the enriched motifs in these ChIP-seq regions.
36 An inbuilt dataset of 10 human OR sub-clusters is available in the TM-MOTIF package for users to assign new sequences to these clusters and to view the alignment in VIBGYOR coloring scheme, along with identified conserved motifs on the alignment.
Background: Mammalian telomeres consist of long tandem arrays of double-stranded TTAGGG sequence motif packaged by TRF1 and TRF2.
For motif detection, we used MEME (Machanick & Bailey 2011) and the peak-motifs package of the Regulatory Sequence Analysis Tools (RSAT) (Thomas-Chollier et al. 2011).
We then took advantage of the existing MOTIPS motif analysis package (Lam et al., 2010) to identify those S. cerevisiae gene products that contain occurrences of the search logo.
The performance of WildSpan in this task is evaluated by investigating the accuracy of function classification by using W-patterns, compared with the curated patterns provided in PROSITE and the patterns discovered by three existing motif finding packages.
While SAPF is used to discover new motifs, the MORPH software package modifies a simple probabilistic aligner to detect and align instances of known motifs that have been previously characterized as position state weight matrices [ 21].
(This is cheating somewhat, since Davis's best-known works deployed advertising and commercial packaging motifs and were painted in what Karen Wilkin describes, in a wall text excerpted from the New Britain Museum's collection catalog, as a "homemade version of Cubism").
For example, the popular motif finding software MEME [4] is packaged with the MAST software [5].
The algorithm consists in translating the six frames for every "pseudomolecule" present in the target genome, followed by a search for HMM (Hidden Markov Models) motifs using the hmmer package (http://hmmer.org).org
