Rahul Nayak
A Bioinformatician
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Cactus: a reference-free whole-genome multiple alignment program
By Jit 2399 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 2078 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...A web-based tool for sequence alignment statistics and innovative visualization
By BioStar 702 days agobioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...Alvis: a tool for contig and read ALignment VISualisation and chimera detection
By LEGE 668 days agogithub.com - Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector...A fast package to parse BLAST
By Jitendra Narayan 4561 days ago, managBlaSTorage: a fast package to parsee and store BLAST resultsBLAST Ring Image Generator (BRIG)
By Anjana 3445 days agobrig.sourceforge.net - BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:...New Layout for BLAST ftp Database Site
By Jit 2237 days ago Comments (1)New Layout for BLAST ftp Database SiteCircoletto: visualizing sequence similarity with Circos
By Jit 2948 days agotools.bat.infspire.org - Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results. Online version and downloadable software package for offline use (source code in...BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2826 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...
