Characterization of subtypes of the influenza A hemagglutinin (HA) gene using profile hidden Markov models

Abstract

We established an analysis framework for assessing sequence-subtype association to provide insights into HA subtypes with close evolutionary relationships.

AIV polyantigen epitope expressed by recombinant baculovirus induces a systemic immune response in chicken and mouse models

“…Human leukocyte antigen (HLA)-A0201 and HLA-1101 were predicted by Bimas (http://bimas.dcrt.nih.gov/molbio/hla_bind/), SYFPEITHI (http://www.uni-tuebingen. de/uni/kxi/), Support Vector Machine (SVM) [5,55], Artificial Neural Network (ANN) [5,17] and Hidden Markov Model (HMM) [16], which presented cytotoxic T lymphocyte epitopes of hemagglutinin of A/NewCaledonia/20/99 (H1N1) (GenBank accession No. INA344014), A/ Netherlands/127/03 (H7N7) (GenBank accession No.…”

Search for Cry proteins expressed by Bacillus spp. genomes, using hidden Markov model profiles

“…database constructed for this purpose, which contains all the registered genomes within this genus. The model was restricted to show only Cry proteins with an e-value lower than 1 × 10E-5 and more than 30% identity, as used earlier (Gong et al 2012;Muñoz-Medina et al 2015).…”

“…These models have been successfully applied on sequence analyses, discovery of genes, and characterization of protein families (Restrepo-Montoya et al 2011). One HMM profile is statistically and probabilistically intrinsic, which is ideal to quantitatively evaluate if an individual sequence belongs to a given profile (Gong et al 2012). HMM profiles have been widely used in the protein families Pfam database, which makes possible to search, classify, and characterize protein families.…”

Genomic profiles of Pseudomonas aeruginosa gene clusters based on profile HMMs, reveal novel therapeutic targets for clinical intervention

“…Tel: +254706350662. Author(s) agree that this article remain permanently open access under the terms of the Creative Commons Attribution License 4.0 International License intensive, and may give negative results if changes occur due to mutations in the biofilm formation genes (Gong et al, 2012). In the last few years P. aeruginosa sequences have become increasingly available, so that a database search and pair-wise comparisons are alternative ways of characterizing them.…”

“…Profile HMMs have previously been used to molecularly detect viruses within metagenomic data, search for Cry proteins expressed by Bacillus spp. genomes and characterize the subtypes of HA gene (Gong et al, 2012;Skewes et al, 2014;Castillo-Esparza et al, 2019).…”