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The genome of Trypanosoma brucei encodes eleven Puf proteins whose function cannot be predicted by sequence analysis.
Overall, our observations and those of Kachroo et al. (2015) suggest that complementation cannot be predicted by sequence similarity.
Cis-regulatory elements can be predicted by sequence conservation analysis, as tight clusters of functional TFBSs can be under strong evolutionary constraint [ 4- 7].
Such cross-hybridizations can result from (i) duplications of genes or short repeated sequences (such as di- or trinucleotide arrays) which can be predicted by sequence analysis, and from (ii) the existence of transcribed sequences (pseudo-genes, disabled CDS or relics) in intergenic regions that may resemble to actual gene sequences [ 37, 38].
The presence of a secondary substrate-binding site cannot easily be predicted by sequence comparisons alone since it depends not only on the characteristics of the residues in this region but also on the conformation of the loop connecting helix α2′ and helix α1, which we term the "second-site loop".
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Seven B cell epitopes (B-P1 to B-P7) were predicted by sequence and structure based methods.
Ribosomal RNAs were predicted by sequence similarity searching using BLAST against an RNA sequence database and/or using Infernal and Rfam models.
Several physical characteristics of the proteins were predicted by sequence analysis and compared to the expression levels.
A number of kinases are predicted by sequence homology to be incapable of phosphoryl group transfer due to degradation of their catalytic motifs.
Three open reading frames (ORFs) were predicted by sequence analysis of the nucleotide sequence and by comparing results with the genomic organization and ORFs of other vesiviruses.
These interactions were predicted by sequence analyses throughout the human genome, in order to identify potential TFBSs and miRNA target sequences (see Section 2).
More suggestions(15)
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