SyntenyTracker protocols

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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

Documentation


Maintainer


This tool is not available anymore.

Publication for SyntenyTracker

SyntenyTracker in pipeline

2016
PMCID: 5010900
PMID: 27401172
DOI: 10.1093/gbe/evw166

[…] 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 […]


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SyntenyTracker in publications

 (7)
PMCID: 5598925
PMID: 28910296
DOI: 10.1371/journal.pone.0179112

[…] scoring of ppis, thus, in turn, refining the general ppi map used in studies like these., 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) […]

PMCID: 5521730
PMID: 28175287
DOI: 10.1093/gbe/evw276

[…] 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 […]

PMCID: 5010900
PMID: 27401172
DOI: 10.1093/gbe/evw166

[…] (supplementary table s1, supplementary material online). sfs were defined using three sets of parameters to detect genome rearrangements that are ≥500, ≥300, and ≥100 kb in the chicken genome with syntenytracker ()., breakpoint regions (brs) were defined as the intervals delimited by two adjacent sf boundaries on the same reference chromosome. we developed a new multi-step approach to detect […]

PMCID: 4772474
PMID: 26927851
DOI: 10.1038/srep22426

[…] allele and informative snps., 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 […]

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

[…] in birds, we first generated a map of the sites of avian syntenic disruption (sd) likely representing chromosomal breakpoints, by comparing the syntenic order of zebra finch vs. chicken genes in syntenytracker. we manually verified the consistency of the synteny groups with previous reports [, ], using our curated ensembl models to allow for a more precise identification of genes […]


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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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