PMC:1635699 / 22403-23293 JSONTXT

{"project":"2_test","denotations":[{"id":"17062125-12520045-1688923","span":{"begin":107,"end":109},"obj":"12520045"},{"id":"17062125-15608160-1688924","span":{"begin":110,"end":112},"obj":"15608160"},{"id":"17062125-12095421-1688925","span":{"begin":281,"end":283},"obj":"12095421"},{"id":"17062125-10329189-1688926","span":{"begin":770,"end":772},"obj":"10329189"},{"id":"17062125-15296519-1688927","span":{"begin":773,"end":775},"obj":"15296519"}],"text":"For the construction of reference alignments we used \"seed\" alignments from the Rfam database version 7.0 [24,23]. In most cases these alignments are hand-curated and thus of higher quality than Rfam's \"full\" alignments generated automatically by the INFERNAL RNA profile package [40]. Alignments with less than 50 sequences were discarded to increase the possibility for creation of subalignments (see below). The SCI (see below) for scoring of structural alignment quality is based on a combination of thermodynamic and covariation measures. Thermodynamic structure prediction becomes increasingly inaccurate with increasing sequence length – e. g. due to kinetic effects – but is widely regarded as sufficiently accurate for sequences not exceeding 300 nt in length [41,42]. Thus we excluded alignments with an average sequence length above 300 nt to ensure proper thermodynamic scoring."}