LedezmaTejeida-Lab/PutrescineAsSignalingMetabolite-v1.0.zip
LedezmaTejeida-Lab-PutrescineAsSignalingMetabolite-71ff41c
.Rhistory
142 Bytes
1_BBH_TFs
BLASTresults
ECaaq_RZaadb_blastP_b1_m8.tab
206.0 kB
ECaaq_RZaadb_blastP_b1_m8_v2.tab
253.4 kB
ECgene_len.tsv
136.1 kB
Orthologous_ECaaq_RZaadb_blastP_b1_m8.tab
130.8 kB
Orthologous_RZaaq_ECaadb_blastP_b1_m8.tab
135.3 kB
RZaaq_ECaadb_blastP_b1_m8.tab
299.1 kB
RZaaq_ECaadb_blastP_b1_m8_v2.tab
366.1 kB
RZgene_len.tsv
215.2 kB
TFs_ECaaq_RZaadb_blastP_b1_m8.tab
7.7 kB
TFs_RZaaq_ECaadb_blastP_b1_m8.tab
7.9 kB
ECdb
GCF_000005845.2_ASM584v2_protein.faaed
1.8 MB
GCF_000005845.2_ASM584v2_protein.faaed.phr
605.2 kB
GCF_000005845.2_ASM584v2_protein.faaed.pin
34.4 kB
GCF_000005845.2_ASM584v2_protein.faaed.psd
87.8 kB
GCF_000005845.2_ASM584v2_protein.faaed.psi
2.0 kB
GCF_000005845.2_ASM584v2_protein.faaed.psq
1.3 MB
RZdb
GCF_000268285.2_RPHCH2410v2_protein.faaed
2.4 MB
GCF_000268285.2_RPHCH2410v2_protein.faaed.phr
703.7 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.pin
49.7 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psd
127.9 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psi
2.8 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psq
1.9 MB
annotation
RZ_functional_annotation.tsv
417.2 kB
RZ_functional_annotation_v2.tsv
264.1 kB
TFs_coli_v2.txt
1.1 kB
merge_annotation.tsv
389.8 kB
bin
R
merge_Etables_p1_v3.R
5.0 kB
merge_Etables_p2_v4.R
3.1 kB
merge_Etables_p3_v5.R
3.7 kB
merge_coverage_BLAST.R
3.1 kB
merge_motif_seq_v2.R
3.6 kB
results_section1.R
1.6 kB
section1-Figures.R
7.5 kB
bash
BBH_TFs.sh
16.7 kB
python
motifs_seq_relation_v2-Parser.py
1.7 kB
error.log
0 Bytes
formatdb.log
2.7 kB
genomesInfo
EC
GCF_000005845.2_ASM584v2_genomic.fna
4.7 MB
GCF_000005845.2_ASM584v2_protein.faa
1.8 MB
RZ
GCA_000268285.2_RPHCH2410v2_genomic.gtf
6.1 MB
GCF_000268285.2_RPHCH2410v2_cds_from_genomic.fna
7.2 MB
GCF_000268285.2_RPHCH2410v2_genomic.fna
6.8 MB
GCF_000268285.2_RPHCH2410v2_genomic.fna.fai
1.1 kB
GCF_000268285.2_RPHCH2410v2_genomic.gbff
16.5 MB
GCF_000268285.2_RPHCH2410v2_genomic.gff
3.2 MB
GCF_000268285.2_RPHCH2410v2_protein.faa
2.4 MB
metabolitesInfo
TFs_metabolites.txt
8.3 kB
motifsInfo
gene_aa_seq.tsv
1.4 MB
motifs_seq_relation.tsv
338.2 kB
motifs_seq_relation_v2.tsv
358.6 kB
motifs_seq_relation_v3.tsv
660.7 kB
ortologousInfo
allOrthologousID.tsv
39.9 kB
png
.Rhistory
66 Bytes
MainF1.png
100.2 kB
SuppF2.png
80.7 kB
tables
Orthologous_ECaaq_RZaad_BLASTid_protein.tsv
70.2 kB
Orthologous_RZ_annotation.tsv
84.1 kB
Orthologous_RZaad_ECaaq_BLASTid_protein.tsv
77.9 kB
Orthologous_table.tsv
2.1 MB
Rplots.pdf
3.8 kB
TF_Orthologous_table.tsv
97.9 kB
2_MotifConservation
BLASTresultsSeq
ECaaq_RZaadb_blastP_b1_m0_seq.txt
13.6 MB
RZaaq_ECaadb_blastP_b1_m0_seq.txt
17.9 MB
ECdb
GCF_000005845.2_ASM584v2_protein.faaed
1.8 MB
GCF_000005845.2_ASM584v2_protein.faaed.phr
605.2 kB
GCF_000005845.2_ASM584v2_protein.faaed.pin
34.4 kB
GCF_000005845.2_ASM584v2_protein.faaed.psd
87.8 kB
GCF_000005845.2_ASM584v2_protein.faaed.psi
2.0 kB
GCF_000005845.2_ASM584v2_protein.faaed.psq
1.3 MB
RZdb
GCF_000268285.2_RPHCH2410v2_protein.faaed
2.4 MB
GCF_000268285.2_RPHCH2410v2_protein.faaed.phr
703.7 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.pin
49.7 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psd
127.9 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psi
2.8 kB
GCF_000268285.2_RPHCH2410v2_protein.faaed.psq
1.9 MB
bin
R
AllMotifs-processing.R
6.0 kB
motifConservationAnalysis.R
2.2 kB
results_section2.R
4.9 kB
section2-MainFigure2.R
6.3 kB
section2-piechartFigure.R
5.2 kB
bash
2_MotifConservation.sh
10.2 kB
python
ECaaq-BLASTseqParser-queID.py
606 Bytes
ECaaq-BLASTseqParser-subjID.py
779 Bytes
ECaaq-BLASTseqParser.py
2.0 kB
ECaaq-MiddleDash-parser.py
1.2 kB
RZaaq-BLASTseqParser-queID.py
606 Bytes
RZaaq-BLASTseqParser.py
1.7 kB
RZaaq-MiddleDash-parser.py
1.2 kB
error.log
0 Bytes
formatdb.log
1.4 kB
formated
ECaaq-queID.tsv
115.7 kB
ECaaq-subjID.tsv
65.8 kB
ECaaqID_temp.tsv
144.4 kB
ECaaq_RZaadb_blastP_seq.tab
1.8 MB
ECaaq_RZaadb_blastP_seq_formated.tsv
1.7 MB
ECaaq_RZaadb_blastP_seq_formated_v2.tsv
1.6 MB
RZaaq-queID.tsv
189.3 kB
RZaaqID_temp.tsv
227.8 kB
RZaaq_ECaadb_blastP_seq.tab
2.5 MB
RZaaq_ECaadb_blastP_seq_formated.tsv
2.3 MB
RZaaq_ECaadb_blastP_seq_formated_v2.tsv
2.2 MB
TF_Orthologous_table.tsv
97.9 kB
genomesInfo
EC
GCF_000005845.2_ASM584v2_genomic.fna
4.7 MB
GCF_000005845.2_ASM584v2_protein.faa
1.8 MB
RZ
GCA_000268285.2_RPHCH2410v2_genomic.gtf
6.1 MB
GCF_000268285.2_RPHCH2410v2_cds_from_genomic.fna
7.2 MB
GCF_000268285.2_RPHCH2410v2_genomic.fna
6.8 MB
GCF_000268285.2_RPHCH2410v2_genomic.fna.fai
1.1 kB
GCF_000268285.2_RPHCH2410v2_genomic.gbff
16.5 MB
GCF_000268285.2_RPHCH2410v2_genomic.gff
3.2 MB
GCF_000268285.2_RPHCH2410v2_protein.faa
2.4 MB
motifsInfo
ECaaq_oTFs_DNAbinding_motifs_info.tsv
2.8 kB
ECaaq_oTFs_motifs_info.tsv
7.0 kB
RZaaq_oTFs_DNAbinding_motifs_info.tsv
2.8 kB
RZaaq_oTFs_motifs_info.tsv
7.0 kB
Rplots.pdf
3.8 kB
motifsConservationIdent30.tsv
4.2 kB
png
MainF2.png
63.7 kB
SuppF3.png
198.2 kB
3_TRN
OrthologousTFInfo
ECaaq_oTFs_DNAbinding_motifs_info.tsv
2.4 kB
ECaaq_oTFs_motifs_info.tsv
7.0 kB
Orthologous_table.tsv
2.1 MB
RZaaq_oTFs_DNAbinding_motifs_info.tsv
2.4 kB
RZaaq_oTFs_motifs_info.tsv
7.0 kB
TF_Orthologous_table.tsv
97.9 kB
TF_Orthologous_table_filter100Cov30Iden.tsv
1.4 kB
annotation
GCA_000268285.2_genomic.gbff
14.1 MB
GCF_000268285.2_genomic.gbff
17.3 MB
bin
R
DNAbindingFilterTFs100Cov30Ident.R
3.2 kB
merge_MatrixScantmpFiles.R
2.6 kB
oTF-TG-NetworkGenerator.R
6.4 kB
section3-MainFigure4.R
3.1 kB
section3-MainTable1.R
5.9 kB
bash
3_TRN.sh
14.2 kB
python
TG-LocusTag-parsey.py
880 Bytes
matrixes
PSSM-Dataset-v4.0-ed.txt
18.9 kB
PSSM-Dataset-v4.0.txt
68.8 kB
RhizobiumphaseoliOrthologousCutOffIdent30Cov100Matrices.tab
5.0 kB
RhizobiumphaseoliOrthologousMatrices.tab
7.1 kB
networkInfo
network_tf_gene.txt
224.9 kB
output
oTF-TG-TRN-10-5-bgM1.tsv
129.9 kB
scan-result-10-5-50-bgM1.html
15.0 kB
scan-result-10-5-50-bgM1.txt
104.8 kB
output-tmp
matrixes.txt
482 Bytes
scan-result-10-5-50-bgM1-35PSSMs.txt
655.7 kB
scan-result-10-5-50-bgM1.txt
590.8 kB
png
MainF4.png
46.5 kB
scan-result-10-5-50-bgM1.png
8.8 kB
sequences
retrieve-seq-Rhizobium_phaseoli_Ch24-10-50.fna
2.9 MB
retrieve-seq-Rhizobium_phaseoli_Ch24-10-50.fnaed
2.9 MB
retrieve-seq-Rhizobium_phaseoli_Ch24-10-50.fnaed.purged
2.9 MB
tables
MainTab1.tsv
1.1 kB
4_Evidence_Levels
annotation
AHJU02.1.gbff
14.1 MB
bin
R
NodulationHeatmap.R
719 Bytes
bash
4_Evidence_Levels.sh
2.0 kB
python
VenDiagram_v2.py
2.2 kB
symbiosisGenes-parser.py
1.0 kB
input
GeneExpression.tsv
47.5 kB
oTF-TG-TRN-10-5-bgM1.tsv
129.9 kB
png
MainF5.png
46.2 kB
SuppF4.png
35.7 kB
tables
SuppTable2.tsv
2.4 kB
5_BBH_PuuR
bin
R
section5-MainFigure6SuppFig5.R
7.0 kB
bash
5_BBH_PuuR.sh
8.9 kB
docs
Rhizobia
Bradyrhizobiumaustraliense-2721161-GCF_013114825.1-ASM1311482v1
GCA_013114825.1
GCA_013114825.1_ASM1311482v1_genomic.fna
7.5 MB
genomic.gbff
17.0 MB
protein.faa
2.5 MB
GCF_013114825.1
BLAST
Orthologous_PuuRID.tsv
28 Bytes
Rhaaq_RpaadbResult.tsv
82 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
375.8 kB
Rpaaq_RhaadbResult.tsv
82 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
375.1 kB
protein.faaed
2.4 MB
protein.faaed.phr
609.0 kB
protein.faaed.pin
53.2 kB
protein.faaed.psd
130.3 kB
protein.faaed.psi
2.9 kB
protein.faaed.psq
1.9 MB
GCF_013114825.1_ASM1311482v1_genomic.fna
7.5 MB
genomic.gbff
18.6 MB
protein.faa
2.5 MB
Bradyrhizobiumdiazoefficiens-1355477-GCF_004359355.1-ASM435935v1
GCA_004359355.1
GCA_004359355.1_ASM435935v1_genomic.fna
9.0 MB
genomic.gbff
20.6 MB
protein.faa
3.3 MB
GCF_004359355.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
84 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
469.4 kB
Rpaaq_RhaadbResult.tsv
84 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
396.6 kB
protein.faaed
3.1 MB
protein.faaed.phr
788.8 kB
protein.faaed.pin
64.8 kB
protein.faaed.psd
159.2 kB
protein.faaed.psi
3.6 kB
protein.faaed.psq
2.5 MB
GCF_004359355.1_ASM435935v1_genomic.fna
9.0 MB
genomic.gbff
23.0 MB
protein.faa
3.2 MB
Bradyrhizobiumjaponicum-375-GCF_013752735.1-ASM1375273v1
GCA_013752735.1
GCA_013752735.1_ASM1375273v1_genomic.fna
9.3 MB
GCF_013752735.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
84 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
481.2 kB
Rpaaq_RhaadbResult.tsv
84 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
396.2 kB
protein.faaed
3.1 MB
protein.faaed.phr
791.4 kB
protein.faaed.pin
67.6 kB
protein.faaed.psd
166.3 kB
protein.faaed.psi
3.7 kB
protein.faaed.psq
2.6 MB
GCF_013752735.1_ASM1375273v1_genomic.fna
9.3 MB
genomic.gbff
22.9 MB
protein.faa
3.2 MB
Rhizobiumetli-29449-GCF_002119845.1-ASM211984v1
GCA_002119845.1
GCA_002119845.1_ASM211984v1_genomic.fna
6.8 MB
genomic.gbff
16.3 MB
protein.faa
2.4 MB
GCF_002119845.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
83 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
469.1 kB
Rpaaq_RhaadbResult.tsv
83 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
464.8 kB
protein.faaed
2.3 MB
protein.faaed.phr
581.0 kB
protein.faaed.pin
49.6 kB
protein.faaed.psd
121.4 kB
protein.faaed.psi
2.7 kB
protein.faaed.psq
1.9 MB
GCF_002119845.1_ASM211984v1_genomic.fna
6.8 MB
genomic.gbff
16.8 MB
protein.faa
2.4 MB
Rhizobiumleguminosarum-384-GCF_004306555.1-ASM430655v1
GCA_004306555.1
GCA_004306555.1_ASM430655v1_genomic.fna
7.7 MB
genomic.gbff
17.6 MB
protein.faa
2.7 MB
GCF_004306555.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
83 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
519.4 kB
Rpaaq_RhaadbResult.tsv
83 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
458.3 kB
protein.faaed
2.7 MB
protein.faaed.phr
683.3 kB
protein.faaed.pin
56.5 kB
protein.faaed.psd
138.6 kB
protein.faaed.psi
3.1 kB
protein.faaed.psq
2.2 MB
GCF_004306555.1_ASM430655v1_genomic.fna
7.7 MB
genomic.gbff
20.0 MB
protein.faa
2.7 MB
SinorhizobiumfrediiCCBAU25509-1128330-GCF_003177055.1-ASM317705v1
GCA_003177055.1
GCA_003177055.1_ASM317705v1_genomic.fna
6.9 MB
genomic.gbff
14.1 MB
protein.faa
2.6 MB
GCF_003177055.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
84 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
416.5 kB
Rpaaq_RhaadbResult.tsv
84 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
422.7 kB
protein.faaed
2.3 MB
protein.faaed.phr
558.9 kB
protein.faaed.pin
48.1 kB
protein.faaed.psd
117.4 kB
protein.faaed.psi
2.6 kB
protein.faaed.psq
1.8 MB
GCF_003177055.1_ASM317705v1_genomic.fna
6.9 MB
genomic.gbff
17.5 MB
protein.faa
2.3 MB
Sinorhizobiummeliloti2011-1286640-GCF_000346065.1-ASM34606v1
GCA_000346065.1
GCA_000346065.1_ASM34606v1_genomic.fna
6.8 MB
genomic.gbff
16.2 MB
protein.faa
2.5 MB
GCF_000346065.1
BLAST
Orthologous_PuuRID.tsv
30 Bytes
Rhaaq_RpaadbResult.tsv
84 Bytes
Rhaaq_Rpaadb_blastP_b1_m8.tab
426.2 kB
Rpaaq_RhaadbResult.tsv
84 Bytes
Rpaaq_Rhaadb_blastP_b1_m8.tab
421.6 kB
protein.faaed
2.3 MB
protein.faaed.phr
559.7 kB
protein.faaed.pin
48.1 kB
protein.faaed.psd
117.6 kB
protein.faaed.psi
2.6 kB
protein.faaed.psq
1.9 MB
GCF_000346065.1_ASM34606v1_genomic.fna
6.8 MB
genomic.gbff
17.4 MB
protein.faa
2.3 MB
RhizobiumPhaseoli
RhizobiumphaseoliCh24-10-1128399-GCF_000268285.2-GCA_000268285.2
GCA_000268285.2
GCA_000268285.2_RPHCH2410v2_genomic.fna
6.8 MB
genomic.gbff
14.1 MB
protein.faa
2.5 MB
GCF_000268285.2
BLAST
protein.faaed
2.4 MB
protein.faaed.phr
606.1 kB
protein.faaed.pin
50.0 kB
protein.faaed.psd
122.3 kB
protein.faaed.psi
2.8 kB
protein.faaed.psq
1.9 MB
GCF_000268285.2_RPHCH2410v2_genomic.fna
6.8 MB
formatdb.log
220 Bytes
genomic.gbff
17.3 MB
protein.faa
2.4 MB
formatdb.log
480 Bytes
multiple_aligment
PuuR-BBH-sequences.dnd
490 Bytes
PuuR-BBH-sequences.faa
2.0 kB
output
MP_BootstrapTreeFilea.tre
827.2 kB
PuuR-BBH-sequences_cluAln.nex
3.5 kB
PuuR-BBH.log
16.1 kB
PuuR-BBH.tree
1.9 kB
Rhaaq_Rpaadb_PuuROrthologous.tsv
584 Bytes
Rpaaq_Rhaadb_PuuROrthologous.tsv
584 Bytes
bootstrap_trees.tre
388 Bytes
png
MainF6.png
63.0 kB
SuppF5.png
77.4 kB
README.Rmd
2.8 kB
README.md
3.5 kB
pipeline.png
80.8 kB
references.bib
2.1 kB