This approach allows to facilitate the generic feature of sequence diagrams as well as an automatic analysis, the identification of the instances of a sequence diagram over a trace.
Paths considered during the computation of this measure are type-path constrained, i.e. they must correspond to instances of a sequence of classes or types named relevance path.
Note that the use of the term "conservation" here is somewhat different from its most common use to describe sequence conservation, but was chosen because it best describes the phenomenon of observing a feature (correlated mutation in this case) in multiple instances of a sequence alignment (such use is not unprecedented, compare for example with the use of "structure conservation").
Of 123 RefSeqs, only seven lack a GA6 sequence at the 5′ end of the pipo ORF (Appendix Dataset S1), while only twelve instances of GA6 sequences were found at other sites within the polyprotein ORFs (Appendix Table S2).
We improved consistency - and significantly improved recall - by tagging all instances of a specific character sequence as a chemical mention if that sequence was tagged by the CRF model at least twice within an abstract.
It is worth noting that there is no universally accepted method for accurately identifying genomic subsequences as being relevant instances of a particular defined sequence motif, and as such, a strictly in silico analysis will always be dependent on choices of method and parameters.
One possibility is that most observed changes between human and chimpanzee occur in sequences that resemble ESRs, but do not in fact play a role in splicing: although some instances of ESRs have been shown to impact splicing patterns in specific contexts, it does not follow that all instances of an ESR-like sequence have true roles in splicing.
We have now identified over 300 instances of a 24-amino-acid sequence region that we designate PEP-CTERM, which has three distinctive sequence features.
Church cautions that editing many instances of a single, repetitive gene sequence isn't the same as targeting many unique genes at once which will be necessary if CRISPR is to become a treatment for complex genetic diseases, for example.
For 1000 instances of a perfectly periodic synthetic sequence of length N = 150 with 10 bp periodicity degraded between 1% and 50% (20 instances per 1% increment), i.e. the true positives, and 1000 randomly permuted instances of the same sequence, i.e. the true negatives, the sensitivity and specificity and hence receiver operator characteristic (ROC) curves were calculated.
400 bp sequences centered on peak summits were extracted from the 119 top-scoring WT Zfp335 peak regions, repeat-masked and used for de novo motif discovery with MEME (parameters: min. width = 6, max. width = 30, zero or one instances of a given motif per sequence).
