Search Results for "genome"

ClustAGE is a command-line tool built using the Perl scripting language for the purpose of analyzing and comparing accessory genomic elements (AGEs) between genomes. It takes as input sets of AGE nucleotide sequences previously identified from the genome sequences of two or more separate organisms. These AGE sequence sets can be extracted from complete or draft whole-genome nucleotide sequences using the previously-developed software tools Spine (https://github.com/egonozer/Spine) and AGEnt (https://github.com/egonozer/AGEnt). See README (https://sourceforge.net/p/clustage/code/ci/master/tree/README.md) for more information.

...The study has collected and continues to collect extensive phenotypic and genotypic detail about its participants, including data from questionnaires, physical measures, sample assays, accelerometry, multimodal imaging, genome-wide genotyping and longitudinal follow-up for a wide range of health-related outcomes. Tofu will generate synthetic data which conforms to the structure of the baseline data UK Biobank sends researchers by generating random values. For categorical variables (single or multiple choices), a random value will be picked from the UK Biobank data dictionary for that field. ...

AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.

Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. ...

quadGT is a software package for the joint genotyping of two parents, child’s normal genome and child’s tumor genome based on sequencing reads aligned to a reference genome.

...It is oriented mainly towards targeted resequencing experiments, with a set of functions for general purposes. BCP also includes a function for breast cancer risk estimation, based on the Gail model, using both clinical and genome data.

genomeLD is a novel bioinformatic tool to simulate linkage disequilibrium (LD) patterns and SNPs for genome-wide association studies.

Contains various algorithms that maps short reads produced from Illumina (Solexa) Genome Analyzer, or Applied Biosystems' SOLiD System, to a reference sequence or a set of reference sequences.