Predicting target DNA sequences of DNA-binding proteins based on unbound structures. [PDF]
PLoS ONE, 2012 DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions.
Chien-Yu Chen +5 more
doaj +1 more source
Base-sequence-dependent sliding of proteins on DNA [PDF]
Physical Review E, 2004 The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general
Barbi, Maria +3 more
openaire +6 more sources
Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2. [PDF]
PLoS ONE, 2011 BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors.
Nina Winter +4 more
doaj +1 more source
A linear model for transcription factor binding affinity prediction in protein binding microarrays. [PDF]
PLoS ONE, 2011 Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a protein's affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity ...
Matti Annala +3 more
doaj +1 more source
A Novel Image Cryptosystem Inspired by the Generation of Biological Protein Sequences
IEEE Access, 2023 Image encryption is essential to keep images secure either in personal devices or over the cloud drives. Various robust image cryptosystems have been implemented during the past decades to keep the encrypted images far from illegal decryption by ...
Mohammad Nassef +2 more
doaj +1 more source
DNA Motif Recognition Modeling from Protein Sequences
iScience, 2018 Summary: Although the existing works on DNA motif discovery on DNA sequences are plethoric, mechanistic knowledge to infer DNA motifs from protein sequences across multiple DNA-binding domain families without conducting any wet-lab experiments is still ...
Ka-Chun Wong
doaj +1 more source
Outline of a genome navigation system based on the properties of GA-sequences and their flanks. [PDF]
PLoS ONE, 2009 Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments.
Guenter Albrecht-Buehler
doaj +1 more source
Peptide vocabulary analysis reveals ultra-conservation and homonymity in protein sequences [PDF]
, 2007 A new algorithm is presented for vocabulary analysis (word detection) in texts of human origin. It performs at 60%–70% overall accuracy and greater than 80% accuracy for longer words, and approximately 85% sensitivity on Alice in Wonderland, a ...
Gatherer, D. +2 more
core +1 more source
Tomato protoplast DNA transformation: physical linkage and recombination of exogenous DNA sequences [PDF]
, 1987 Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication.
Zabel, Pim +11 more
core +1 more source
LIA5 is required for nuclear reorganization and programmed DNA rearrangements occurring during tetrahymena macronuclear differentiation. [PDF]
PLoS ONE, 2013 During macronuclear differentiation of the ciliate Tetrahymena thermophila, genome-wide DNA rearrangements eliminate nearly 50 Mbp of germline derived DNA, creating a streamlined somatic genome.
Annie Wan Yi Shieh, Douglas L Chalker
doaj +1 more source