The legume information system and associated online genomic resources
Abstract The Legume Information System (LIS; https://legumeinfo.org) houses genetic and genomic data, integrated in various online tools to allow comparative genomic analyses. The website and database maintain data for more than two dozen species, particularly focusing on crop and model species and...
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doaj-88581ad44e754a0bae55c177f02a88742021-09-24T12:00:24ZengWileyLegume Science2639-61812021-09-0133n/an/a10.1002/leg3.74The legume information system and associated online genomic resourcesJoel Berendzen0Anne V. Brown1Connor T. Cameron2Jacqueline D. Campbell3Alan M. Cleary4Sudhansu Dash5Samuel Hokin6Wei Huang7Scott R. Kalberer8Rex T. Nelson9Sven Redsun10Nathan T. Weeks11Andrew Wilkey12Andrew D. Farmer13Steven B. Cannon14National Center for Genome Resources Santa Fe NM USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USANational Center for Genome Resources Santa Fe NM USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USANational Center for Genome Resources Santa Fe NM USANational Center for Genome Resources Santa Fe NM USANational Center for Genome Resources Santa Fe NM USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USANational Center for Genome Resources Santa Fe NM USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USAORISE, Corn Insects and Crop Genetics Research Unit USDA‐ARS Ames IA USANational Center for Genome Resources Santa Fe NM USAUSDA‐ARS Corn Insects and Crop Genetics Research Unit Ames IA USAAbstract The Legume Information System (LIS; https://legumeinfo.org) houses genetic and genomic data, integrated in various online tools to allow comparative genomic analyses. The website and database maintain data for more than two dozen species, particularly focusing on crop and model species and holding data for other diverse species of taxonomic interest. Major analysis features include genome browsers, sequence‐search tools, legume‐focused gene families and a phylogenetic tree viewer, a gene annotation service (which places a submitted gene into a gene family and phylogenetic tree), an interactive microsynteny and pan‐genome viewer, a novel viewer of genetic variant data, genetic maps and viewers, a Data Store for data sets such as assemblies and annotations, InterMine instances for querying genetic and genomic data, and a tool for viewing geographic distributions of germplasm accessions. LIS also integrates with several other legume data resources and tools, including PeanutBase (https://peanutbase.org), SoyBase (https://soybase.org), Medicago Hapmap (https://medicagohapmap2.org), Alfalfa Breeder's Toolbox (https://alfalfatoolbox.org), and the Legume Federation (https://legumefederation.org).https://doi.org/10.1002/leg3.74comparative genomicsCoNekTdeterminacygene familiesgenome context viewerInterMine |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Joel Berendzen Anne V. Brown Connor T. Cameron Jacqueline D. Campbell Alan M. Cleary Sudhansu Dash Samuel Hokin Wei Huang Scott R. Kalberer Rex T. Nelson Sven Redsun Nathan T. Weeks Andrew Wilkey Andrew D. Farmer Steven B. Cannon |
spellingShingle |
Joel Berendzen Anne V. Brown Connor T. Cameron Jacqueline D. Campbell Alan M. Cleary Sudhansu Dash Samuel Hokin Wei Huang Scott R. Kalberer Rex T. Nelson Sven Redsun Nathan T. Weeks Andrew Wilkey Andrew D. Farmer Steven B. Cannon The legume information system and associated online genomic resources Legume Science comparative genomics CoNekT determinacy gene families genome context viewer InterMine |
author_facet |
Joel Berendzen Anne V. Brown Connor T. Cameron Jacqueline D. Campbell Alan M. Cleary Sudhansu Dash Samuel Hokin Wei Huang Scott R. Kalberer Rex T. Nelson Sven Redsun Nathan T. Weeks Andrew Wilkey Andrew D. Farmer Steven B. Cannon |
author_sort |
Joel Berendzen |
title |
The legume information system and associated online genomic resources |
title_short |
The legume information system and associated online genomic resources |
title_full |
The legume information system and associated online genomic resources |
title_fullStr |
The legume information system and associated online genomic resources |
title_full_unstemmed |
The legume information system and associated online genomic resources |
title_sort |
legume information system and associated online genomic resources |
publisher |
Wiley |
series |
Legume Science |
issn |
2639-6181 |
publishDate |
2021-09-01 |
description |
Abstract The Legume Information System (LIS; https://legumeinfo.org) houses genetic and genomic data, integrated in various online tools to allow comparative genomic analyses. The website and database maintain data for more than two dozen species, particularly focusing on crop and model species and holding data for other diverse species of taxonomic interest. Major analysis features include genome browsers, sequence‐search tools, legume‐focused gene families and a phylogenetic tree viewer, a gene annotation service (which places a submitted gene into a gene family and phylogenetic tree), an interactive microsynteny and pan‐genome viewer, a novel viewer of genetic variant data, genetic maps and viewers, a Data Store for data sets such as assemblies and annotations, InterMine instances for querying genetic and genomic data, and a tool for viewing geographic distributions of germplasm accessions. LIS also integrates with several other legume data resources and tools, including PeanutBase (https://peanutbase.org), SoyBase (https://soybase.org), Medicago Hapmap (https://medicagohapmap2.org), Alfalfa Breeder's Toolbox (https://alfalfatoolbox.org), and the Legume Federation (https://legumefederation.org). |
topic |
comparative genomics CoNekT determinacy gene families genome context viewer InterMine |
url |
https://doi.org/10.1002/leg3.74 |
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