xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

• Main Authors: Yap, Choon-Kong, Eisenhaber, Birgit, Eisenhaber, Frank, Wong, Wing-Cheong
• Other Authors: School of Computer Science and Engineering
• Format: Article
• Language: English
• Published: 2016
• Subjects: Sequence homology; Hidden Markov model
• Online Access: https://hdl.handle.net/10356/84677; http://hdl.handle.net/10220/41906
• Institution: Nanyang Technological University

Background: 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 insu...