{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Yap CK"],"funding":["A*STAR"],"pagination":["63"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5126834"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(1)"],"pubmed_abstract":["<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 s"],"journal":["Biology direct"],"pubmed_title":["xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation."],"pmcid":["PMC5126834"],"funding_grant_id":["“A*STAR-NKTH JGC 007”, “SERC IMaGIN”, and “IAF CAT3 Integrated Genomics Platform."],"pubmed_authors":["Eisenhaber B","Eisenhaber F","Yap CK","Wong WC"],"additional_accession":[]},"is_claimable":false,"name":"xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.","description":"<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 s","dates":{"release":"2016-01-01T00:00:00Z","publication":"2016 Nov","modification":"2026-06-14T05:49:38.315Z","creation":"2019-03-27T02:30:04Z"},"accession":"S-EPMC5126834","cross_references":{"pubmed":["27894340"],"doi":["10.1186/s13062-016-0163-0"]}}