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Steps to find all the repeats in the genome !
Last updated 451 days ago by NeelTo find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide: Install RepeatMasker: First, you need to install RepeatMasker on your system. You...RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
By Jit 2553 days agokiwi.cs.dal.ca - RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 1483 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesSISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2187 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...RNA Sequencing Helps Identify Functional Variants from GWAS
By Andaleeb 4019 days agoschizophreniaforum.org - For Alzheimer’s and other complex disorders, mining the genome for disease-associated variants is no longer the obstacle. The challenge nowadays is figuring out how the identified loci relate to disease. As reported last month in Nature and...dcGOR
By Martin Jones 3668 days agoan R package for analysing ontologies and protein domain annotationsRASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3132 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3109 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...GAEMR
By Jit 3085 days agowww.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
By Abhimanyu Singh 2887 days agohttp://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...
