{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,21]],"date-time":"2025-12-21T06:24:47Z","timestamp":1766298287420},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Sequence alignment is one of the most popular tools of modern biology. NCBI's PSI-BLAST utilizes iterative model building in order to better detect distant homologs with greater sensitivity than non-iterative BLAST. However, PSI-BLAST's performance is limited by the fact that it relies on deterministic alignments. Using a semi-probabilistic alignment scheme such as Hybrid alignment should allow for better informed model building and improved identification of homologous sequences, particularly remote homologs.<\/jats:p>\n               <jats:p>Results: We have built a new version of the tool in which the Smith-Waterman alignment algorithm core is replaced by the hybrid alignment algorithm. The favorable statistical properties of the hybrid algorithm allow the introduction of position-specific gap penalties in Hybrid PSI-BLAST. This improves the position-specific modeling of protein families and results in an overall improvement of performance.<\/jats:p>\n               <jats:p>Availability: Source code is freely available for download at http:\/\/bioserv.mps.ohio-state.edu\/HybridPSI, implemented in C and supported on linux.<\/jats:p>\n               <jats:p>Contact: \u00a0bundschuh@mps.ohio-state.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq621","type":"journal-article","created":{"date-parts":[[2010,11,26]],"date-time":"2010-11-26T01:14:18Z","timestamp":1290734058000},"page":"31-37","source":"Crossref","is-referenced-by-count":9,"title":["A performance enhanced PSI-BLAST based on hybrid alignment"],"prefix":"10.1093","volume":"27","author":[{"given":"Yuheng","family":"Li","sequence":"first","affiliation":[{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"}]},{"given":"Nicholas","family":"Chia","sequence":"additional","affiliation":[{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"},{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"}]},{"given":"Mario","family":"Lauria","sequence":"additional","affiliation":[{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"}]},{"given":"Ralf","family":"Bundschuh","sequence":"additional","affiliation":[{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"},{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"},{"name":"1 Covidien, 60 Middletown Avenue, North Haven, CT, 06473, 2Institute for Genomic Biology, 1206 West Gregory Drive, 3Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA, 4Systems Biology Group, Telethon Institute of Genetics and Medicine (TIGEM), via P. Castellino 111, 80131 Naples, Italy, 5Department of Physics, Biophysics Graduate Program, The Ohio State University, 191 West Woodruff Avenue, 6Department of Biochemistry, 484 West 12th Avenue and 7Center for RNA Biology, 318 West 12th Avenue, Columbus, OH 43210, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,11,24]]},"reference":[{"key":"2023012511155921900_B1","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/S0076-6879(96)66029-7","article-title":"Local alignment statistics","volume":"266","author":"Altschul","year":"1996","journal-title":"Methods Enzymol."},{"key":"2023012511155921900_B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. 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