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Finding the Hidden Switches: The Story of KiNext and Protein Kinases
By LEGE 12 days agoEvery newly sequenced genome contains thousands of proteins, but identifying what each protein does is a much harder task. Among these proteins are protein kinases, important molecular regulators that control processes such as cell growth,...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 3066 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...CovCal: Coverage / Read Count Calculator
By Jit 3765 days ago Comments (1)apps.bioconnector.virginia.edu - Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration and genome size, then select what you want to calculate. Written by Stephen...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 3226 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2649 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2435 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 381 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 2116 days agogithub.com - The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3235 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...String graph based genome assembly software and tools !
By Rahul Nayak 3213 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.
