Our data model provides the required types and properties to capture experimental details of both the partitioning of non-binding sequences from a sequence library and the recovery of binding sequences from aptamer-target complexes in SELEX experiments.
The most significant binding peaks (FDR ≤ 0.05), which coincided in both replicates, were analyzed by the program RSAT dyad-analysis to predict binding sequence from all peak genomic binding sites [ 36].
If we think of sequences S as vectors in a vector space V and H = { x ∈ V| ε x = -1} a hyperplane separating the binding sequences from the non-binding ones, then H is "supported" by those observed sequences S(a ), which corresponds to non-trivial γ a.
We derive a single refined probabilistic model of STAT1 binding sequences from these ChIP-seq data.
We selected a threshold that identified 90% of Sp1 binding sequences from our experimentally confirmed training set (see Methods).
The consensus TF binding sequences from PLACE, AGRIS and JASPAR were also used to scan TFBSs in a promoter sequence by homemade perl program.
To explore the potential of collagen silk chimera for regulating biological activity, integrin (Int) and fibronectin (Fn) binding sequences from mammalian collagens were introduced into the bacterial collagen domain.
Although methods with limited structural flexibility have proven successful at recapitulating consensus binding sequences from wild-type complex structures, conformational flexibility is likely important for design and template-based modeling, where non-native conformations need to be sampled and accurately scored.
The bovine and rat decoron binding sequences from collagen type I are shown in Table S2.
Matrices from other sources were STAT [69] (from the Transfac 7 database [70]), shn1 and shn2 (the two binding domains of shn, from Dai et al. [71]), Ci (constructed from the consensus sequence TGGGTGGTC, with consensus bases given a weight of 0.85 and the remainder distributed uniformly), Mef2 (from binding sequences from Elgar et al. [72]) and Pnt (from Halfon et al. [73]).
