biostudies-literatureYap CKA*STAR63https://www.ebi.ac.uk/biostudies/studies/S-EPMC5126834biostudies-literatureUnknown11(1)<h4>Background</h4>While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.<h4>Results</h4>In this work, both the speed of HMMER3 and glocal-mode alignment of HMMER2 are combined within the xHMMER3x2 framework for tackling the large-scale domain annotation task. Briefly, HMMER3 is utilized for initial domain detection so that HMMER2 can sBiology directxHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.PMC5126834“A*STAR-NKTH JGC 007”, “SERC IMaGIN”, and “IAF CAT3 Integrated Genomics Platform.Eisenhaber BEisenhaber FYap CKWong WCfalsexHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.<h4>Background</h4>While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.<h4>Results</h4>In this work, both the speed of HMMER3 and glocal-mode alignment of HMMER2 are combined within the xHMMER3x2 framework for tackling the large-scale domain annotation task. Briefly, HMMER3 is utilized for initial domain detection so that HMMER2 can s2016-01-01T00:00:00Z2016 Nov2026-06-14T05:49:38.315Z2019-03-27T02:30:04ZS-EPMC51268342789434010.1186/s13062-016-0163-0