Synteny Portal specifications

Information


Unique identifier OMICS_11706
Interface Web user interface
Restrictions to use None
Input data SynCircos: user-selected reference and target species, genome assembly version of the selected species, chromosome number, a resolution for the synteny blocks and an image format for visualization in the Circos plot; SynBrowser: only four user-selected parameters: a reference species, a reference chromosome, a target species and a synteny block resolution; SynSearcher: a user-provided DNA or protein sequence can be directly inserted in a text box or uploaded as a file in a FASTA format; SynBuilder: the selection of a reference, target and optional outgroup species, and a resolution for the synteny blocks
Output data SynCircos: an interactive Circos plot; SynBrowser: a plot showing connections between homologous blocks between two species and a gene browser displaying reference genes within synteny blocks; SynSearcher: (i) the details of the BLAST output for the top-matched alignment result, (ii) the coordinates of identified pairwise synteny blocks and (iii) a Circos plot visualizing the synteny blocks; SynBuilder: (i) the coordinates of synteny blocks and (ii) an interactive Circos plot depicting syntenic relationships among the chosen species
Programming languages Javascript, Perl, PHP
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • SynCircos
  • SynBrowser
  • SynSearcher
  • SynBuilder

Documentation


Maintainer


  • person_outline Jaebum Kim <>

Synteny Portal article

Synteny Portal institution(s)
Department of Animal Biotechnology, Konkuk University, Seoul, Korea; Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
Synteny Portal funding source(s)
Supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning [2014M3C9A3063544, 2013R1A1A2008183, 2011-619-E0002].

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