CottonGen Synteny Viewer

Metadata Updated: November 10, 2020

Conserved syntenic regions among publicly available cotton genomes were analyzed by CottonGen and made available using the Tripal Synteny Viewer developed by the Fei Bioinformatics Lab from the Boyce Thomson Institute at Cornell University. Analysis was done using MCScanX (Wang et al. 2012) with default settings and blast files were made using blastp with an expectation value cutoff < 1e-10, maximum alignment of 5, and maximum scores of 5. The synteny viewer displays all the conserved syntenic blocks between a selected chromosome of a genome and another genome in a circular and tabular layout. Once a block is chosen in the circular or tabular layout, all the genes in the block are shown in a graphic and tabular format. The gene names have hyperlinks to gene pages where detailed information of the gene can be accessed. The ‘synteny’ section of the gene page displays all the orthologs and the paralogs with link to the corresponding syntenic blocks or gene pages.

Access & Use Information

Public: This dataset is intended for public access and use. License: Creative Commons CCZero

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Dates

Metadata Created Date November 10, 2020
Metadata Updated Date November 10, 2020

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date November 10, 2020
Metadata Updated Date November 10, 2020
Publisher Agricultural Research Service
Unique Identifier Unknown
Maintainer
Identifier 97be3bf4-20b2-4a74-a9e0-a79268470708
Data Last Modified 2019-08-23
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 08b32652-5e1a-4e73-aa0d-c0269ef41602
Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
Harvest Source Title USDA JSON
License https://creativecommons.org/publicdomain/zero/1.0/
Program Code 005:040
Source Datajson Identifier True
Source Hash 0b6f2f8cc56266166d0570b27c33726f92627ff9
Source Schema Version 1.1

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