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In case of alternative transcripts the highest score between any two protein products is saved.
Therefore the reconstructed sequence may not reflect the actual sequences especially in case of alternative splicing events.
In case of alternative splicing forms, the splice selected was the one corresponding to the mature form according to TAIR.
In case of alternative spliceforms, the longest one is kept in the GreenPhylDB pipeline; it is thus the one we downloaded.
* – In case of alternative donor/acceptor sites, the lengths of alternative gene segments were calculated as distance between alternative splice sites.
Since VSL2B provides per-residue predictions, we measure the disorder content, which is defined as the fraction of residues in a protein sequence (or sequence alignment in case of alternative splicing) that is predicted to be disordered.
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In case of alternatives of a cycle (see [ 39]), the intermediates are not copied (being holistic), but the system as a whole may exhibit attractor-based heredity [ 40].
In cases of alternative splicing variants, only a single splice variant was included.
Moreover, the redundancy of the technique [ 38] proved to be very informative in cases of alternative splicing and multigene family member displaying [ 27, 29, 32], for distinguishing highly homologous genes [ 39- 41].
The alternative part can consist of several segments in case of multiple alternative PAS.
In case of fault alternative techniques: In case of failure some alternate signal processing techniques should be developed to overcome the situation in case of occurrence of failure of the existing algorithm.
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