Hydrangea macrophylla

[RaymondS1]

Publication and Data Information

https://academic.oup.com/dnaresearch/advance-article/doi/10.1093/dnares/dsaa026/5974207

Additional Information

Link to genome (HMA_r1.2_1): https://plantgarden.jp/en/list/t23110/genome/t23110.G003

Checklist

See New Genome Documentation for detailed instructions.

• [x] Create Organism
• [x] Create Publication
• [x] Create Reference Genome
• [x] Create InterProScan Annotation
• [x] Create BLAST Annotation
• [x] Run Chado FASTA Loader for CDS
• [x] Run Chado FASTA Loader for Polypeptides
• [x] Publish Tripal content
• [x] Create KEGG Annotation
• [x] Run Chado KEGG Loader
• [x] Run Chado BLAST XML results loader
• [ ] Run Chado InterProScan XML results loader
• [x] Create Blast Database

[RaymondS1]

Organism created: https://hardwoodgenomics.org/bio_data/4302783?tripal_pane=group_summary_tripalpane

• Deleted

Old Organism: https://hardwoodgenomics.org/organism/Hydrangea/macrophylla?tripal_pane=group_summary_tripalpane

[RaymondS1]

Swissprot

#PBS -N swissprot_BLAST
#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-200
#PBS -l nodes=1:ppn=2
#PBS -l walltime=12:00:00

cd $PBS_O_WORKDIR

module load blast

blastx \
 -query /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/raw_data/BLAST_splits/HMA_r1.2_1.cds.fasta.$PBS_ARRAYID \
 -db /lustre/haven/proj/UTK0032/library/uniprot/uniprot_sprot.fasta \
 -out /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/BLAST/swissprot/macrophylla_swissprot.$PBS_ARRAYID.xml \
 -evalue 1e-5 \
 -outfmt 5

[RaymondS1]

Trembl

#PBS -N trembl_BLAST
#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-200
#PBS -l nodes=1:ppn=2
#PBS -l walltime=12:00:00

cd $PBS_O_WORKDIR

module load blast

blastx \
 -query /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/raw_data/BLAST_splits/HMA_r1.2_1.cds.fasta.$PBS_ARRAYID \
 -db /lustre/haven/proj/UTK0032/library/uniprot/uniprot_trembl_plants_July_2018.fasta \
 -out /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/BLAST/trembl/macrophylla_trembl.$PBS_ARRAYID.xml \
 -evalue 1e-5 \
 -outfmt 5

[RaymondS1]

IPS

#PBS -N hydrangea_ips
#PBS -A ACF-UTK0011
#PBS -S /bin/bash
#PBS -t 1-500
#PBS -j oe
#PBS -l nodes=1:ppn=4
#PBS -l walltime=18:00:00

cd $PBS_O_WORKDIR

module load python3

/lustre/haven/proj/UTK0032/software/interproscan-5.34-73.0/interproscan.sh \
 -i /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/raw_data/IPS_splits/HMA_r1.2_1.protein.fasta.$PBS_ARRAYID \
 -f XML \
 -d /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/IPS/xmls \
 --disable-precalc \
 --iprlookup \
 --goterms \
 --pathways \
 --tempdir /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/IPS/TMP \
 > /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/IPS/TMP/$PBS_ARRAYID.out

[RaymondS1]

Publication Created https://hardwoodgenomics.org/Publication/4302784

[RaymondS1]

Reference Genome https://hardwoodgenomics.org/Genome-assembly/4302785

[RaymondS1]

Files to be loaded to the site

CDS: /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/raw_data

Protein: /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/raw_data/HMA_r1.2_1.protein.fasta

Swissprot /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/BLAST/swissprot/xml

Trembl /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/BLAST/trembl/xml

IPS /lustre/haven/proj/UTK0032/projects/undergrads/hydrangea_macrophylla/IPS/xmls

[noah-77]

FTP downloads available at https://hardwoodgenomics.org/Genome-assembly/4302785?tripal_pane=group_downloads