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SOLiD ToP Sequencing chemistry was used to produce paired-end (50 bp + 35 bp) sequencing reads.
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All currently leading protein secondary structure prediction methods use a multiple protein sequence alignment to predict the secondary structure of the top sequence.
In most of these methods, prior to prediction, alignment positions showing a gap in the top sequence are deleted, consequently leading to shrinking of the alignment and loss of position-specific information.
Table 3 only presents the top sequences identified in each of the situations.
The wild-type S16 and L30 TOP sequences were replaced by the TOP sequence of L32.
The TOP sequence of S16 and L30 was also introduced into the L32 5' UTR (Fig. 6C).
Strikingly, mutating the TOP sequence in the L32 5' UTR abrogated its responsiveness to eIF4E (Fig 6A).
An interesting possibility is that only a subset of TOP sequences confers differential eIF4E responsiveness.
The top sequence matches to the genus of these genomes and the percentage of ORF hits to each are shown.
However, all other sequences were unique to the source and were not found in other samples; 59% of all the top sequences were of fecal origin (Figure 2).
Related to Figure S5C top sequence.
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