A benchmark of multiple sequence alignment programs upon structural RNAs Export

@article{Gardner2005, abstract = {To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current algorithms, is generally inappropriate <50-60\% sequence identity. Second, we note that the probabilistic method ProAlign and the aging Clustal algorithms generally outperform other sequence-based algorithms, under the broadest range of applications. 10.1093/nar/gki541}, author = {Gardner, P. P. and Wilm, A. and Washietl, S.}, booktitle = {Nucl. Acids Res.}, citeulike-article-id = {203341}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gki541}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/33/8/2433}, citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/nar/2005/00000033/00000008/art02433}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/15860779}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=15860779}, day = {28}, doi = {10.1093/nar/gki541}, issn = {0305-1048}, journal = {Nucleic Acids Research}, keywords = {alignment, evaluation, method}, month = {April}, number = {8}, pages = {2433--2439}, posted-at = {2009-05-24 21:57:41}, priority = {0}, publisher = {Oxford University Press}, title = {A benchmark of multiple sequence alignment programs upon structural RNAs}, url = {http://dx.doi.org/10.1093/nar/gki541}, volume = {33}, year = {2005} }

TY - JOUR ID - Gardner2005 L3 - citeulike-article-id:203341 N2 - To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current algorithms, is generally inappropriate <50-60% sequence identity. Second, we note that the probabilistic method ProAlign and the aging Clustal algorithms generally outperform other sequence-based algorithms, under the broadest range of applications. 10.1093/nar/gki541 IS - 8 JF - Nucleic Acids Research SN - 0305-1048 EP - 2439 TI - A benchmark of multiple sequence alignment programs upon structural RNAs PB - Oxford University Press VL - 33 T2 - Nucl. Acids Res. SP - 2433 KW - alignment KW - evaluation KW - method AU - Gardner, PP AU - Wilm, A AU - Washietl, S PY - 2005/04/28/ UR - http://dx.doi.org/10.1093/nar/gki541 ER -