Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: An enhanced RNA alignment benchmark for sequence alignment programs. | Algorithms for Molecular Biology BioMed Central Research Open Access An enhanced RNA alignment benchmark for sequence alignment programs Andreas Wilm Indra Mainz and Gerhard Steger Address Institut fur Physikalische Biologie Heinrich-Heine-Universitat Dusseldorf Universitatsstr. 1 40225 Dusseldorf Germany Email Andreas Wilm - wilm@ Indra Mainz - mainzi@ Gerhard Steger - steger@ Corresponding author Published 24 October 2006 Received 30 August 2006 Algorithms for Molecular Biology 2006 1 19 doi 1748-7188-1-19 Accepted 24 October 2006 This article is available from http content 1 1 19 2006 Wilm et al licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background The performance of alignment programs is traditionally tested on sets of protein sequences of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem as was demonstrated in the first RNA alignment benchmark published so far. For example the twilight zone - the similarity range where alignment quality drops drastically - starts at 60 for RNAs in comparison to 20 for proteins. In this study we enhance the previous benchmark. Results The RNA sequence sets in the benchmark database are taken from an increased number of RNA families to avoid unintended impact by using only a few families. The size of sets varies from 2 to 15 sequences to assess the influence of the number of sequences on program performance. Alignment quality is scored by two measures one takes into account only nucleotide matches the other measures structural conservation. The performance order of parameters - like .
