{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:03:50Z","timestamp":1773270230913,"version":"3.50.1"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Multiple sequence alignment is an essential part of bioinformatics tools for a genome-scale study of genes and their evolution relations. However, making an accurate alignment between remote homologs is challenging. Here, we develop a method, called SPEM, that aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment.<\/jats:p>\n               <jats:p>Results: The alignment accuracy of SPEM is compared with those of established methods such as ClustalW, T-Coffee, MUSCLE, ProbCons and PRALINEPSI in easy (homologs) and hard (remote homologs) benchmarks. Results indicate that the average sum of pairwise alignment scores given by SPEM are 7\u201315% higher than those of the methods compared in aligning remote homologs (sequence identity &amp;lt;30%). Its accuracy for aligning homologs (sequence identity &amp;gt;30%) is statistically indistinguishable from those of the state-of-the-art techniques such as ProbCons or MUSCLE 6.0.<\/jats:p>\n               <jats:p>Availability: The SPEM server and its executables are available on http:\/\/theory.med.buffalo.edu<\/jats:p>\n               <jats:p>Contact: \u00a0yqzhou@buffalo.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti582","type":"journal-article","created":{"date-parts":[[2005,7,15]],"date-time":"2005-07-15T00:13:59Z","timestamp":1121386439000},"page":"3615-3621","source":"Crossref","is-referenced-by-count":70,"title":["SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures"],"prefix":"10.1093","volume":"21","author":[{"given":"Hongyi","family":"Zhou","sequence":"first","affiliation":[]},{"given":"Yaoqi","family":"Zhou","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2005,7,14]]},"reference":[{"key":"2023060912062004800_B1","doi-asserted-by":"crossref","unstructured":"Altschul, S.F., et al. 1997Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 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