Abstract MOTIVATION: Locating protein-coding exons (CDSs) on a eukaryotic genomic DNA sequence is the initial and an essential step in predicting the funct... G Osamu - 《Bioinformatics》 被引量: 112发表: 2000年 Summarizing a set of time series by averaging: From Steiner sequence to compact ...
I am doing DNA sequence alignment using DECIPHER (AlignSeqs). I am getting the error in the second step (Clustering into groups by similarity:) alignmentFls <- AlignSeqs(DNAStringSet(seqFls), processors=NULL, anchor=NA) Determining distance matrix based on shared 7-mers: |===| 100% Time...
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules—proteins, RNAs and DNAs. The pipeline is built on a uniform TM-score object...
Teeling H, Lombardot T, Bauer M, Ludwig W, Glockner FO: Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Micro...
DNA or protein sequences. The design of the model allows for a direct connection between the scoring function and the parameters of the probabilistic model. For this reason it is suitable to analyze the outcomes of popular score based aligners and search tools without having to choose a ...
Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding ... JK Hane,RP Oliver - 《Bmc Bioinformatics》 被引量: 210发表: 2008年 PROKARYOTE PHYLOGENY WITHOUT SEQUENCE ALIGNMENT:: FROM AVOIDANCE SIGNATUR...
In short, the ligand source protein was split into overlapping peptide sequences of the length of the ligand. All peptides except the annotated HLA ligand were taken as negatives. This is a very strong assumption since suboptimal peptides that could be presented on the HLA molecule are counted...
Conventional Methods for Aligning Sequence Reads FIG. 1 is a schematic illustration of a conventional NGS sequencing and data analysis workflow, in accordance with various embodiments. As depicted herein, a NGS sequencer102sequences a plurality of genomic (DNA or RNA) fragments obtained from a biolo...
In some aspects, agents may be a nucleic acid molecule, for example, any nucleic acid containing molecule, including but not limited to, DNA or RNA. The term encompasses sequences that include any of the known base analogs of DNA and RNA including, but not limited to, 4-acetylcytosine, ...
“U.S. Appl. No. 11/543,515, filed Oct. 24, 2006, Micron Ref. No. 2005-1173.00/US.” Ex Parte Cantell, unpublished decision of the Board of Patent Appeals and Interferences, Mar. 4, 2005. Choi et al., “Sublithographic nanofabrication technology for nanocatalysts and DNA chips,” J...