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. ...

...Please refer to: https://github.com/suhrig/pingpongpro Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs, predominantly active in the germ line. There, they limit the detrimental effect of transposons on the genome. They do so by forming a complex with Piwi proteins. The complex binds and then cleaves mRNA molecules of active transposons. The resulting mRNA fragments induce the production of more piRNAs, thus reinforcing the anti-transposon response in a feed-forward loop called the "ping-pong cycle". A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. ...

Chiu et. al., Genome Research 2014 Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. We showed that our integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines.

...DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It was developed in order to assess the DNA methylation variations within a cell population for a given genomic locus or genome-wide methylation data.

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.

Framework for editors development

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.