• JASPAR

  • Referenced in 40 articles [sw18502]
  • programming tools for genome‐wide and comparative genomic analysis of regulatory regions. JASPAR is available...
  • LAGAN

  • Referenced in 17 articles [sw13192]
  • alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN...
  • OrthoMCL

  • Referenced in 14 articles [sw29602]
  • genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences...
  • BioHMM

  • Referenced in 13 articles [sw10920]
  • method (BioHMM) for segmenting array comparative genomic hybridization data into states with the same underlying...
  • BEDTools

  • Referenced in 11 articles [sw17302]
  • flexible suite of utilities for comparing genomic features. Motivation: Testing for correlations between different sets ... comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature ... compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation...
  • CNV-seq

  • Referenced in 11 articles [sw17970]
  • important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used...
  • CGH-Plotter

  • Referenced in 9 articles [sw07372]
  • with a graphical user interface for comparative genomic hybridization (CGH) data analysis. The CGH-Plotter...
  • BLAT

  • Referenced in 34 articles [sw16891]
  • BLAST-Like Alignment Tool. Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments ... alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT’s speed stems from ... nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers ... compared with other alignment programs on various test sets and then used in several genome...
  • PathBLAST

  • Referenced in 7 articles [sw29737]
  • network alignment and search tool for comparing protein interaction networks across species to identify protein ... enables rapid comparison of protein sequences between genomes ... tools such as PathBLAST are enabling comparative genomics at the network level...
  • PipMaker

  • Referenced in 7 articles [sw17257]
  • Genomic DNA Sequences. PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing ... plot). PipMaker is appropriate for comparing genomic sequences from any two related species, although...
  • MetaCyc

  • Referenced in 28 articles [sw08243]
  • organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical networks, and serving...
  • MSOAR

  • Referenced in 6 articles [sw29658]
  • critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts...
  • CONFAC

  • Referenced in 4 articles [sw35535]
  • CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. The advent ... unique opportunity for the integration of comparative genomics with high-throughput gene expression analysis. Here ... CONFAC software compares non-coding regulatory sequences between human and mouse genomes to enable identification ... promoters of gene clusters from microarray analyses compared to sets of unchanging control genes using...
  • curvclust

  • Referenced in 6 articles [sw07435]
  • functional data analysis on microarray comparative genomic hybridization (CGH) data. Our procedure is available through...
  • REDfly

  • Referenced in 5 articles [sw29315]
  • well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies...
  • QUAST

  • Referenced in 4 articles [sw17094]
  • tool for genome assemblies. Summary: Limitations of genome sequencing techniques have led to dozens ... methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem ... quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly ... this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables...
  • CGHclassify

  • Referenced in 4 articles [sw17253]
  • Array-based comparative genomic hybridization (aCGH). aCGH Clone Classification R Software...
  • Circos

  • Referenced in 4 articles [sw27740]
  • Circos: an information aesthetic for comparative genomics. We created a visualization tool called Circos...
  • cghseg

  • Referenced in 4 articles [sw06783]
  • profiles The statistical analysis of array comparative genomic hybridization (CGH) data has now shifted...
  • GASTS

  • Referenced in 3 articles [sw29624]
  • study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models...