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The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position
El-Sherif lab studies how genes are regulated to mediate patterning in Development. We use live and super-resolution imaging in addition to computational modeling to understand transcription dynamics at the single-cell level in three model systems:...
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 2313 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...Common methods to discover tandem repeats
By BioStar 1306 days agoTandem repeats are DNA sequences that are repeated in a contiguous manner in the genome.SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 748 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
By Abhimanyu Singh 2924 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...Genomic Basis of Evolutionary Innovations (GEvol)
By BioStar 302 days agog-evol.uni-muenster.de - The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“ GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one...Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
By Jit 3237 days agosourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer...
By Surabhi Chaudhary 3067 days agobmcgenomics.biomedcentral.com - SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in...minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
By Jit 3028 days agogithub.com - git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi...
