Resources of LGPR

Sources

Data	Reference	Website	Download
Pearl millet genomic sequence and its derivatives	Varshney et al., 2017, Nat Biotechnol, 35: 969-976	Sequencing Consortium NCBI Genome	Whole genome sequence GFF file Genome-derived gene sequences Genome-derived transcript (CDS) sequences Genome-derived protein sequences Genome-derived 5-kb promoter sequences
Pearl millet transcript sequences derived from RNA sequencing	Shinde et al., 2018, Environ Exp Bot, 155: 619-627	NA	Transcript sequences
Pearl millet gene annotation	Tsugama et al., 2021, BMC Res Notes, 14: 181	This website	BLASTP result and annotations with Arabidopsis protein information BLASTP result and annotations with rice protein information Pfam hit list PANTHER hit list ELM hit list BLASTN result with hairpin-type miRNA database
Pearl millet RNA-Seq-derived TPM values	Kambara et al., 2023	This website	TPM values for all pearl millet genes with many samples
Garden asparagus genomic sequence and its derivatives	Harkess et al., 2017, Nat Commun, 8: 1279	Genome Project NCBI Genome	Whole genome sequence GFF file Genome-derived gene sequences Genome-derived transcript (CDS) sequences Genome-derived protein sequences Genome-derived 5-kb promoter sequences
Garden asparagus transcript sequences derived from RNA sequencing	Harkess et al., 2015, New Phytol, 207: 883-892	Dryad Digital Repository	Transcript sequences
Garden asparagus gene annotation	Tsugama et al., 2019	This website	BLASTP result and annotations with Arabidopsis protein information BLASTP result and annotations with rice protein information Pfam hit list PANTHER hit list ELM hit list BLASTN result with hairpin-type miRNA database
BLAST programs	Altschul et al., 1997, Nucleic Acids Res, 25: 3389-3402 (for BLASTN, BLASTP, BLASTX, TBLASTN) Zhang et al., 2000, J Comput Biol, 7(1-2): 203-214 (for MEGABLAST)	NCBI BLAST download website	See the NCBI website
JBrowse	Skinner et al., 2009, Genome Res, 19: 1630-1638 Buels et al., 2016, Genome Biol, 17: 66	JBrowse website	See the JBrowse website
Arabidopsis gene sequences and annotations	Swarbreck et al., 2008, Nucleic Acids Res, 36: D1009-D1014	TAIR	See the TAIR website
Rice gene sequences and annotations	Ouyang et al., 2007, Nucleic Acids Res, 35: D883-D887 (for Rice Genome Annotation Project (RGAP)) Kurata and Yamazaki, 2006, Plant Physiol, 140: 12-17 (for Oryzabase)	RGAP Oryzabase	See the RGAP and Oryzabase websites
Pfam entries	El-Gebali et al., 2019, Nucleic Acids Res, 47: D427-D432	Pfam website	See the Pfam website
PANTHER entries	Mi et al., 2019, Nucleic Acids Res, 47: D419-D426	PANTHER website	See the PANTHER website
ELM (Eukaryotic Linear Motif) entries	Gouw et al., 2018, Nucleic Acids Res, 46: D428-D434	ELM website	See the ELM website

TGIF-DB — Terse Genomics Interface for Developing Botany

TGIF-DB
— Terse Genomics Interface for Developing Botany