Jit
Enthusiast computational biologist with business dream !!!
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Elastic BLAST !
By Abhi 809 days agoblast.ncbi.nlm.nih.gov - ElasticBLAST is a new way to BLAST large numbers of queries, faster and on the cloud. Here are the top three reasons you should use ElasticBLAST: 1. ElasticBLAST can handle much LARGER queries! ElasticBLAST can search query...Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
By Jit 1348 days agoprakharg24.github.io - We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2542 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2366 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
By Jit 2283 days agowww.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...Cactus: a reference-free whole-genome multiple alignment program
By Jit 1930 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...The wavefront alignment (WFA) algorithm
By BioStar 1609 days agogithub.com - The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in...CNIDARIA: fast, reference-free phylogenomic clustering
By Shruti Paniwala 3082 days agogithub.com - Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 2538 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1668 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...
