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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:...NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
By Jit 2345 days agogithub.com - NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly...SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 749 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: creates an interactive, two-dimensional heatmap of sequences
By Jit 2930 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...MMseqs2.0: ultra fast and sensitive protein search and clustering suite
By Jit 3120 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The...dcGOR
By Martin Jones 4350 days agoan R package for analysing ontologies and protein domain annotationsiSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2424 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...
Tools for Searching Repeats And Palindromic Sequences
Last updated 3095 days ago by Poonam Mahapatra Comments (2)What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...gSearch: a fast and flexible general search tool for whole-genome sequencing
By Jit 2983 days agoml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...YASS :: genomic similarity search tool
By Jit 3809 days agobioinfo.lifl.fr - YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST,...
