PMC:1635699 / 1170-2025 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1635699","sourcedb":"PMC","sourceid":"1635699","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1635699","text":"Conclusion\nMost sequence alignment programs perform equally well on RNA sequence sets with high sequence identity, that is with an average pairwise sequence identity (APSI) above 75 %. Parameters for gap-open and gap-extension have a large influence on alignment quality lower than APSI ≤ 75 %; optimal parameter combinations are shown for several programs. The use of different 4 × 4 substitution matrices improved program performance only in some cases. The performance of iterative programs drastically increases with increasing sequence numbers and/or decreasing sequence identity, which makes them clearly superior to programs using a purely non-iterative, progressive approach. The best sequence alignment programs produce alignments of high quality down to APSI \u003e 55 %; at lower APSI the use of sequence+structure alignment programs is recommended.","divisions":[{"label":"title","span":{"begin":0,"end":10}}],"tracks":[]}