• TOUCAN

  • Referenced in 2 articles [sw17181]
  • regulatory sequence analysis on metazoan genomes: comparative genomics, detection of significant transcription factor binding sites ... remotely access multiple algorithms for comparative genomics, motif detection, and module detection. 2005, TOUCAN...
  • SCARPA

  • Referenced in 6 articles [sw12608]
  • addition to a simulated diploid genome and compare its performance with several state...
  • rSW-seq

  • Referenced in 3 articles [sw17971]
  • copy number alterations in a tumor genome compared to its matched control, based on application ... region for 1X genome coverage of the human genome. We further refine the algorithm ... human cancer genome. To validate our approach, we compare our algorithm with an existing algorithm ... simulated and publicly available datasets. We also compare the sequencing-based profiles to microarray-based...
  • UniProt

  • Referenced in 129 articles [sw21320]
  • with the majority of sequences coming from genome sequencing projects. We have created ... best characterized and most informative for comparative analysis. All UniProt data is provided freely...
  • BEETL

  • Referenced in 5 articles [sw23284]
  • Comparing DNA sequence collections by direct comparison of compressed text indexes. Popular sequence alignment tools ... such as BWA convert a reference genome to an indexing data structure based ... that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions ... Code to construct and compare the BWT of large genomic data sets is available...
  • PyCogent

  • Referenced in 3 articles [sw26797]
  • have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework...
  • Rnaz

  • Referenced in 3 articles [sw17118]
  • detection of structured noncoding RNAs in comparative genomics data. Four years of experience have...
  • RSEM

  • Referenced in 11 articles [sw17160]
  • superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage...
  • PerM

  • Referenced in 4 articles [sw35278]
  • improve mapping efficiency for large reference genomes when compared with state-of-the-art programs ... bytes per base to index the human genome, allowing entire genomes to be loaded...
  • EDGAR

  • Referenced in 1 article [sw08337]
  • EDGAR - A software platform for comparative genomics. The introduction of next generation sequencing approaches ... comparative approach. A main task in comparative genomics is the identification of orthologous genes ... different genomes and the classification of genes as core genes or singletons. To support these ... studies EDGAR - ”Efficient Database framework for comparative Genome Analyses using BLAST score Ratios” - was developed...
  • eHive

  • Referenced in 2 articles [sw27408]
  • eHive: An Artificial Intelligence workflow system for genomic analysis. We present eHive, a new fault ... processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed...
  • INFUSE

  • Referenced in 2 articles [sw02950]
  • requirements. par The proposed demonstration studies Comparative Genomics as one Information Fusion scenario. Gene information...
  • S-Cluster++

  • Referenced in 2 articles [sw29662]
  • containment problem for phylogenetic networks. Motivation: Comparative genomic studies indicate that extant genomes are more...
  • FLLat

  • Referenced in 2 articles [sw19127]
  • multi-sample aCGH data. Array-based comparative genomic hybridization (aCGH) enables the measurement...
  • PhyloCSF

  • Referenced in 1 article [sw11719]
  • PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Motivation ... coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence ... species Drosophila genome alignments exceeds all other methods we compared in a previous study...
  • CGHMultiArray

  • Referenced in 1 article [sw35534]
  • exact P-values for multi-array comparative genomic hybridization data. We compute P-values, based ... compare two conditions with array comparative genomic hybridization data, and we provide a simple interface...
  • GenomeDiagram

  • Referenced in 1 article [sw24774]
  • visualization of large-scale genomic, comparative genomic and other data with reference to a single...
  • i-ADHoRe

  • Referenced in 1 article [sw29669]
  • homology in extremely large data sets. Comparative genomics is a powerful means to gain insight ... related species. As the number of sequenced genomes increases, the development of software to perform ... implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements...
  • GOtcha

  • Referenced in 4 articles [sw17189]
  • Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned ... GOtcha method is a useful tool for genome annotators. It has identified both errors...
  • GRASS

  • Referenced in 4 articles [sw12609]
  • called scaffolds. Most existing scaffolders of HTS genome assemblies are not suited for using information ... programming approximation of the original problem. We compared GRASS with existing HTS scaffolders using Illumina ... reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes ... additional data, in the form of related genome sequences, are used. Availability: GRASS source code...