When overlaying our sequencing data from the L. donovani exosome RNA library with a recently sequenced L. donovani spliced leader (SL) RNA library (P. Myler, unpublished data), we observed that the genomic loci giving rise to our identified novel transcripts had SL sites in the 5′ region upstream of them (see Figure 4 for 2 examples).
By overlaying the sequence of pictures through time in Photoshop (ADOBE), the movement of the turf algae-coral boundary could be quantified (i.e., as speed in mm 3 wk−1 and as absolute direction toward/away from the coral).
Figure 5 pictures this alignment display, along with two curves overlaying the sequence information.
Insights can be obtained by overlaying other sequence-specific information on the tree, including mutation frequencies [ 82], selection strengths [ 83], number of mRNAs observed [ 12], isotype [ 13, 14], or tissue location [ 9, 12, 77].
The Rv2745c sequence predicts a helix-turn-helix DNA-binding motif [34], [38], and by overlaying the Rv2745c protein sequence on a recently published structure of the Corynebacterium glutamicum ClgR protein [38], [39], [40] we identified residues with predicted direct DNA interactions.
Consistent with their sequence similarity, overlaying the structures of the isolated PR72 subunit and the PR70 from the holoenzyme shows that they share a similar structural core encompassing the two EF hand calcium-binding motifs, with a root-mean-square-deviation of 1.44 Å over 262 residues.
The net result is the identification of probes that directly overlay polymorphic sequences.
I have added a paragraph to address this: An obvious alternative to ab initio inference of orthologous relationships is to start with an existing reference database of putative orthologs or homologs such as OMA [ 102], MBGD [ 103], EggNOG [ 104] and OrthoMCL [ 105] as a scaffold, and overlay new sequences to the existing reference sets.
An obvious alternative to ab initio inference of orthologous relationships is to start with an existing reference database of putative orthologs or homologs such as OMA [ 102], MBGD [ 103], EggNOG [ 104] or OrthoMCL [ 105] as a scaffold, and overlay new sequences to the existing reference sets.
Overlaying experimental data (e.g. sequence variation) onto curated tracks (e.g. gene predictions) allows for the formulation and verification of biological hypotheses.
The motif was identified by overlaying the binding sites of Zfp57, Kap1 and Setdb1, identified by separate ChIP-seq experiments, and computing the consensus sequence over all sites occupied by all three proteins.
