• R/qtl

  • Referenced in 13 articles [sw20451]
  • genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans...
  • HapMix

  • Referenced in 6 articles [sw33847]
  • markers; but, using all markers from genome-wide scanning arrays, it should in principle...
  • HEGESMA

  • Referenced in 2 articles [sw10468]
  • comprehensive software for performing genome scan meta-analysis, a quantitative method to identify genetic regions ... consistently increased linkage score across multiple genome scans, and for testing the heterogeneity...
  • ChromoScan

  • Referenced in 3 articles [sw35412]
  • ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies ... ChromoScan is an implementation of a genome-based scan statistic that detects genomic regions, which...
  • RNASurface

  • Referenced in 1 article [sw23120]
  • data, development of computational methods to survey genomes for structured RNAs remains an actual problem ... available for comparative analysis. Existing programs scan genomes with a fixed window by efficiently constructing ... present an algorithm RNASurface to efficiently scan genomes by constructing a matrix of significance...
  • tess3r

  • Referenced in 1 article [sw25205]
  • estimating ancestry coefficients and for running genome scans for selection...
  • LEA

  • Referenced in 1 article [sw25208]
  • analyses of population structure and genome scans for local adaptation. It includes statistical methods...
  • PASS

  • Referenced in 3 articles [sw35276]
  • each other. After building the genomic index, the program scans every query sequence performing three ... finds matching seed words in the genome; (2) for every match checks the precomputed alignment...
  • METAL

  • Referenced in 2 articles [sw28171]
  • tool for meta-analysis of genome-wide association scans, which is a commonly used approach...
  • N-SCAN

  • Referenced in 2 articles [sw17458]
  • stated as follows: given an alignment of genomic sequences from two or more organisms, predict ... Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem ... entire human genome. An analysis of the predictions reveals that N-SCAN’s predictive accuracy ... genome of the fruit fly Drosophila melanogaster to demonstrate the applicability of N-SCAN...
  • LocusZoom

  • Referenced in 1 article [sw29110]
  • regional visualization of genome-wide association scan results. Genome-wide association studies (GWAS) have revealed...
  • xMAN

  • Referenced in 1 article [sw35339]
  • integers hashed in RAM, xMAN can scan through genomes using bit shifting operation and achieve...
  • SUPERFAMILY

  • Referenced in 5 articles [sw16889]
  • functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection ... produced by scanning protein sequences from over 2,478 completely sequenced genomes against the hidden...
  • FIMO

  • Referenced in 6 articles [sw17298]
  • Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described ... Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning...
  • MCScanX

  • Referenced in 1 article [sw29671]
  • MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify...
  • MiRFinder

  • Referenced in 3 articles [sw29577]
  • software implementation for genome-wide fast microRNA precursor scans. Background: MicroRNAs (miRNAs) are recognized ... called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related...
  • QTLRel

  • Referenced in 0 articles [sw15231]
  • missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci...
  • Rnall

  • Referenced in 1 article [sw23119]
  • suitable for RNA LSS prediction on the genome scale due to high computational complexity. METHODS ... based on a dynamic programming technique, which scans an RNA sequence with a sliding window ... facilitate RNA motif mining on the genomic scale. RESULTS: Rnall shows better prediction accuracy than ... also applied to scan for RNA LSSs in three genomes, and the prediction maps well...
  • snoSeeker

  • Referenced in 1 article [sw15009]
  • programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified...
  • mrMLM

  • Referenced in 0 articles [sw15963]
  • each position (or marker) on the genome is scanned using random-SNP-effect mixed linear...