A new generation of homology search tools based on probabilistic inference.

By Sean R. Eddy. 2009

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In Molecular Biology

Citations in the corpus

HH-suite3 for fast remote homology detection and deep protein annotation (2019, methodology): “Therefore, to find template proteins for comparative protein structure modeling and for deep functional annotation, the most sensitive search tools such as HMMER [3, 4] and HHblits [5] are often used [6–9].”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, methodology): “1b package [ Eddy, 2009 ]).”
Large-scale determination of previously unsolved protein structures using evolutionary information (2015, methodology): “N 8, [ Eddy, 2009 ]) with uniref100 database ( Suzek et al., 2007 ) from January, 2015 and eliminated identical sequences and sequences aligned over less than 75% of the protein; the number of remaining sequences for each of the 58 families is listed in Table 2 .”
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts (2014, methodology): “In brief, an ab initio hidden Markov model (HMM), representing the multiple sequence alignment of homologous (both orthologous and/or paralogous) sequences within the Swis-sProt/TrEMBL [16] database, is constructed using the HMMER3 [17] software suite.”
Phytozome: a comparative platform for green plant genomics (2011, methodology): “Multiple sequence alignments of each family’s founding members are created using MUSCLE, and the alignments are used by HMMER3 to create hidden Markov model profiles.”
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. (2012, methodology): “Second, the putatively noncoding transcripts and the ‘‘gray’’ set transcripts were repeat-masked and subjected to blastx, blastp, and HMMER (versus Pfam-A and Pfam-B) (Eddy 2009).”
Evaluation of methods for modeling transcription-factor sequence specificity (2013, methodology): “We identified the DNA Binding Domain (DBD) of each TF by searching for Pfam domains 51 using the HMMER tool 52 .”