Tools

Annotation

• LIS Transcript/Protein Functional Annotation Tool (bring your sequences, we'll asssign them to families and even add them into trees for you!)
• Annotate your sequences: https://legumeinfo.org/annot

Sequence Search

• KnowPulse Sequence Search
• Search for sequences in diverse legumes: https://legumeinfo.org/blast
• Search for sequences in peanut and relatives: https://peanutbase.org/blast
• Keyword search for features in genome browsers: https://legumeinfo.org/keyword_search

Genes and Gene Families

• Search for gene families and annotations by gene name: https://legumeinfo.org/search/gene
• Search for gene families by family characteristic: https://legumeinfo.org/search/phylotree
• LIS Gene Families Search (with access to interactive gene tree visualizations and multiple protein sequence alignments)

Synteny

• LIS Syntenic Genomic Context Viewer (all the genomes in legumeinfo, in all their syntenic glory!)

Germplasm

• LIS Geographic Germplasm Viewer (germplasm collection and trait evaluation data, displayed according to their world geographic distribution)
• View germplasm collections geographically: https://legumeinfo.org/germplasm/map
• SoyBase GRIN Data Explorer

Genetic Markers

• CSFLDB Marker Search
• Search and view soybean SNPs: https://www.soybase.org/snps/index.php
• GO term enrichment analysis for soybean: https://soybase.org/goslimgraphic_v2/

Genetic Maps and Genome Viewers

• Genetic Map viewers:

  • CMap-js Currently under beta testing: (Display and compare biological maps including genetic, physical, cytogenetic, genomic, linkage groups, chromosomes, scaffolds)
  • CSFLdb Map Viewer (Graphical tool for viewing and comparing genetic maps)

• Whole genome feature viewers:

  • CViT (Chromosome Visualization Tool) is a Perl utility for generating images of features on a whole genome)
  • CViTjs (Javascript tool for quick whole-genome views)

• Classic genome viewers:

  • GBrowse
  • JBrowse
  • IGV A tool for interactive exploration of large, integrated genomic datasets

QTLs

• QTL and trait search in various legumes: https://legumeinfo.org/search/qtl
• QTL and trait search in peanut: https://peanutbase.org/search/qtl

Expression

• eFP browser for peanut: http://bar.utoronto.ca/efp_arachis/cgi-bin/efpWeb.cgi

Genetic Variant Data

• Genome-wide views of genetic variants (SNPs) between accessions in bean: https://gcvit.phaseolus.legumeinfo.org
• Genome-wide views of genetic variants (SNPs) between accessions in chickpea: https://gcvit.cicer.legumeinfo.org
• Genome-wide views of genetic variants (SNPs) between accessions in soybean: https://soybase.org/gcvit/

GWAS

• ZBrowse: interactive GWAS viewer

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