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Citations per year

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Protocols

SyntenyTracker specifications

Information


Unique identifier OMICS_11731
Name SyntenyTracker
Interface Web user interface
Restrictions to use None
Input data Pair-wise RH or gene-based comparative maps
Programming languages Perl
Computer skills Basic
Stability No
Maintained No

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Publication for SyntenyTracker

SyntenyTracker citations

 (7)
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The impact of the protein interactome on the syntenic structure of mammalian genomes

2017
PLoS One
PMCID: 5598925
PMID: 28910296
DOI: 10.1371/journal.pone.0179112
call_split See protocol

[…] Orthology-based conserved syntenic blocks were defined in two steps with an approach inspired by Cinteny [], SyntenyTracker [] and i-ADHoRe [,]. First, pairwise syntenic blocks were defined by comparing the order of orthologous protein-coding genes in the human genome (assembly GRCh37.p8) with the chimpanzee […]

call_split

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia

2016
Genome Biol Evol
PMCID: 5521730
PMID: 28175287
DOI: 10.1093/gbe/evw276
call_split See protocol

[…] n the genomes of the mouse (NCBIm37 assembly) and 11 representative species of mammalian phylogeny by Satsuma Synteny () (, online). Based on the sequence alignments provided by Satsuma Synteny, the SyntenyTracker algorithm () was used to establish regions of homology (syntenic regions) between the mouse genome (reference genome) and each of the mammalian species included in the analysis based on […]

library_books

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles

2016
Genome Biol Evol
PMCID: 5010900
PMID: 27401172
DOI: 10.1093/gbe/evw166

[…] mes. To avoid genes that could be located in mis-assembled parts of both genomes or have erroneous definitions of orthology in Ensembl, we used the gene list to build chicken–human pairwise HSBs with SyntenyTracker using the gene coordinates. This allowed the detection of “singleton” and “out-of-place” genes located in unexpected positions within or between HSBs. These genes were removed from furt […]

call_split

Identification of Loci Modulating the Cardiovascular and Skeletal Phenotypes of Marfan Syndrome in Mice

2016
Sci Rep
PMCID: 4772474
PMID: 26927851
DOI: 10.1038/srep22426
call_split See protocol

[…] The synteny analysis was carried out using the Mouse Map Converter application, to convert the QTL regions (cM) to physical distance intervals (bp), and the SyntenyTracker to identify the homology blocks between the mouse and human genomes. The existence of human homologues associated with diseases affecting MFS-related organ systems was verified with the […]

library_books

Comparative genomics reveals molecular features unique to the songbird lineage

2014
BMC Genomics
PMCID: 4377847
PMID: 25494627
DOI: 10.1186/1471-2164-15-1082

[…] ed to be of type “ortholog_one-to-one” in both Zebra finch (taeGut3.2.4) and Chicken (WASHUC2, May 2006). We only included genes with known physical locations in both genomic assemblies. We then used SyntenyTracker [] in Orthologous Gene Pair mode with default settings (i.e. distance between markers 1 Mb, block size 0 bp, block length 2 Mb, jumping distance 2 Mb, reference genome “Zebra finch,” ta […]

call_split

Unraveling the effect of genomic structural changes in the rhesus macaque implications for the adaptive role of inversions

2014
BMC Genomics
PMCID: 4082625
PMID: 24969235
DOI: 10.1186/1471-2164-15-530
call_split See protocol

[…] in Figure . In order to detect the evolutionary breakpoint regions (EBRs) and homologous synteny blocks (HSBs) between human and macaque whole-genome sequences, two different algorithms were applied: SyntenyTracker [] and Cassis []. Both approaches compare the order and orientation of orthologous markers (genes) between genomes, detecting changes both in the sequence order and the position of the […]


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SyntenyTracker institution(s)
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
SyntenyTracker funding source(s)
The United States Department of Agriculture Cooperative State Research Education and Extension service (AG 2005-34480-15939).

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