Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between...
Fourth, adding non-protein modalities (e.g. non-coding regulatory elements) as input to gLM may also greatly improve gLM’s representation of biological sequence data, and can learn protein function and regulation conditioned upon other modalities51. Finally, our model was trained largely on ...
utilizing DDL2, expanded data categories and attributes to reflect the complexity of macromolecular structure studies, including support for protein and nucleic acid polymer types, polymer chains, ligands,binding sites,macromolecular assemblies,amino acidand nucleotide residues, atomic coordinates, and ...
To determine the structural organization ofPmMSP1, nucleotide diversity was determined across the aligned complete coding sequences of 35 Thai isolates and the sequence from a Cameroonian patient (GenBank accession no. FJ824669) whose nucleotide and amino acid positions of the gene/protein were used...
Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD (2014) Current status and new features of the consensus coding sequence database. Nucleic Acids Res 42:D865...
To: nucleotide sequence of the reference sequence starting with 1. 6. Name The name of the reference sequence as given in the input alignment. 7. Start The nucleotide position in the reference sequence of the 8. End predicted coding region. If no genomic coordinates are given (if you ...
The same was true for a number of the other candidates and may account for the high percentage of genes with no significant E-value returns to the Uniprot protein database [86]. There is increasing evidence for the role of riboregulators, either as long non-protein coding RNAs or processed...
Identifying functional effects of noncoding variants is a major challenge in human genetics. DeepSEA developed by Zhou et al. could directly learn a regulatory sequence code from large-scale chromatin-profiling data, enabling prediction of chromatin effects of sequence alterations with single-nucleotide ...
3 Nucleotide sequence of the GhAPm promoter region. The transcription and translation sites are indicated with the arrows. The putative core promoter consensus sequences and cis-acting elements mentioned are boxed Fig. 4 The predicted 3-D structure of GhAPm. The N-terminal domain is part of ...
and to come up with an optimal statement of homology, nucleotide sequences were visualized in Seaview 4.2.7 [51] and then converted to amino acid sequences for alignment with MAFFT [52] under L-INS-i algorithm, thereby preserving the open reading frame for these protein coding sequences. Am...