Therefore, we used similarity-based clustering and sensitive similarity searches.
Using sensitive similarity search methods, we identified statistically significant sequence similarities among several transmembrane protein families including alkaline ceramidases and PAQRs.
This "Trait to Gene" software (TTG in the sequel) identifies 33 COGs as associated with flagella phenotype at the most sensitive similarity threshold 0.65.
To unravel the history of the plant PRC1 complex, we performed sensitive similarity searches and subsequently inferred phylogenetic trees for its subunits.
Furthermore, we take the scale-sensitive similarities between parts into the evaluation of matching values, and extend the original VSM to a relaxed matching framework.
The context similarity effect in the HF was relatively small, perhaps because HF patterns are more sensitive to similarities in object context associations than to context alone (Hsieh et al., 2014; Libby et al., 2014).
In particular, the rejection of fitting the PM model to RA data (PM-RA) with the decay kernel, and fitting the RA model to PM data (RA-PM) with the delay kernel, is extremely sensitive to similarity of stimuli and data size.
The approach developed in the present study is an amalgamation of searches in enriched databases derived from proteins with known structure and sensitive remote similarity detection algorithms.
Using spaced seeds is proven to be more sensitive in similarity detection while maintaining the same specificity compared to searching by exact strings [ 33].
During a sensitive sequence-similarity search for transcription elongation factors in an evolutionary wide range of organisms, we noticed high-scoring hits for Elf1 in a subset of archaeal predicted proteomes.
One specific goal of this study is to test whether the number of detected TEs is low in the clean set of experimentally-characterized protein sequences despite the use of sensitive sequence similarity measures.
