Membrane proteins with cytosolic N-termini were aligned such that the first residue of TM-X (X = 1 5) is aligned to position 0. The frequency of codons having programmed pauses in every position was analyzed, similar to Figure 2D.
For each position we determined whether the condition was true, where the predicate E(X i, Y j ) is defined as meaning position i in sequence X is aligned to position j in sequence Y.
For a pair of linked fragment attractors g a and g b and one of their shared fragments f1, position k in f1 may be aligned to position i in fragment attractor g a and position j in g b.
(A ) Membrane proteins were aligned such that the first residue of TM2 is aligned to position 0 (red line).
(C ) B. subtilis membrane proteins were aligned such that the first residues of TM1 or TM2 or TM3 are aligned to the position 0. The percentage of codons having pauses in every position was analyzed.
Suppose that two adjacent sequence positions are aligned to two template positions j1 and j2 (j2> j1+1), respectively.
When the motif with highest significance is found, all of its non-overlapping occurrences in the first set of sequences are aligned to create a position specific probability matrix.
Given that we know a priori which positions in a profile alignment are allowed to bear a selenocysteine, selenoprofiles favors the alignment to UGA codons only if these are aligned to one such position.
Positions that match the same profile position are aligned to each other, and positions that do not match the profile are removed.
Likewise, lone reads are considered duplicates if they are aligned to the same position.
However, once the motif with the highest significance has been found, all of its non-overlapping occurrences in the first set of sequences are aligned to create a position-specific probability matrix (Stormo, 2000).
