INDELVAR, a random forest model for in-frame insertions and deletions of 1-10 amino acids that integrates 37 features describing AlphaFold-derived wild-type structural context, evolutionary conservation, local sequence change, gene constraint, and curated protein annotations, is developed.
Background Comparisons between independently predicted wild-type and missense-variant protein structures can generate mechanistic hypotheses, but small apparent differences may reflect model-selection variability rather than mutation-specific effects. Methods Human mitochondrial DNA polymerase gamma (POLG; UniProt P540...
Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach becau...
Swethasree Bhattaram, D. Bhowmik, Ramakrishnan Kannan· Proceedings of the 32nd ACM...· 0 citations
ContextSV, a framework that integrates alignment evidence with copy number predictions derived from sequencing coverage and single-nucleotide variant allele frequencies to improve SV detection, serves as a valuable complement to existing long-read SV detection approaches by improving sensitivity for large and clinicall...
J. E. Perdomo, Mian Umair Ahsan, Jasmine Akoto et al.· NAR Genomics and Bioinformat...· 0 citations
EnZight is a user-friendly web server that integrates homologous structural alignment with intuitive visualization to identify substitution hotspots in protein cores that enables prediction of substitutions that preserve fold integrity while modulating function and thermostability.
Rune R. Østergaard, Mikkel Lyskjær Jensen, Suzana Siebenhaar et al.· bioRxiv· 0 citations
A simple generative approach for creating synthetic 5′-UTR libraries based solely on the genomic sequence statistics of any desired organism and demonstrates that simple statistical language model approaches applied to genomic data can generate functional translational regulatory sequence libraries without detailed mec...
A. Duggan, M. Newman, David R. McMillen· PLoS ONE· 0 citations
This work describes the full spectrum of genetic variation and shows that while 99% of the variants between any two genomes are single base-pair substitutions, 88% of the euchromatic variant base pairs are SVs, including insertions, deletions, duplications, and inversions.
J. Lin, J. Gustafson, J. Wertz et al.· medRxiv· 1 citation
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
