The first type of tree was generated by complement alignment of the sequences using ClustalX [ 73], and computing the pairwise distance-matrix of the aligned sequences with PHYLIP software package [ 74].
In that case, generic information is generated by OpenBabel and complemented by querying the PubChem database.
Complemented p65 NIH 3T3 MEFs stably expressing p65 wild type or the acetylation-deficient mutants were generated by lentiviral complementation as previously described in [ 18].
Thereafter, a synthetic miR* was generated by taking the reverse complement of the synthetic miR sequence, adding a random two-nucleotide 3′ overhang sequence and introducing bulges in the duplex by random mutation of the synthetic miR* sequence, with a probability of 0.2 per nucleotide.
For each human 3′-UTR reference sequence, the allelic complement was generated by replacing every reference allele with the nonreference allele at each bi-allelic polymorphic locus reported by 1000G.
Again assume that only lethal mutations occur, albeit a lethal mutation on the non-transcribed strand (NTS) does not manifest an effect until its complement is generated by replication using products made from the transcribed strand of the infecting genome.
Also, we give a characterization on a Toeplitz operator for which the orthogonal complement of its kernel is generated by certain inner functions.
The complement lines for OsINV3 were generated by incorporation of this vector into the homozygous Tos17 mutant using Agrobacterium (EHA105) mediated transformation (Toki 1997).
A more-comprehensive approach is to complement the simulated data with experimental data, which was generated by the previous studies and is publicly available.
To complement the sven0913, sven0914, and sven0915 deletion mutants, PCR products were generated by high-fidelity PCR using the primers listed in Table S1 in the supplemental material.
