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View BLAST Sequence Analysis

BLAST

Transcriptome Libraries vs nr Database

Command: blastall -p blastx -i ../HvCatNor7_Trans.fasta -d /data/process/DBs/nr -e 1e-3 -o HvCatNorvsnr.txt -a 15

Transcriptomevsnr.png

1. Hv701_Trans.fasta vs nr
Screen_shot_2012-03-21_at_11.51.10_AM.png

2. Hv955_Trans.fasta Vs Nr
Screen_shot_2012-04-09_at_12.16.39_PM.png

3. HvCatNor7_Trans.fasta vs Nr
Screen_shot_2012-03-29_at_2.27.55_PM.png

Puccinia Rusts vs Transcriptome Libraries

Task assigned on Tunebo Server

  • Path of DBs: /data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/DBs/
  • Path of Query’s: /data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/
  • Working Path: /data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/

BLASTx RESULTS

Data Files:

1. Puccinia striiformis f. sp. tritici Predicted Proteins (22,815 seqs): bio@ticuna:/data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/Protein_DBs/Pstriiformis_proteins.fasta: Downloaded from http://maswheat.ucdavis.edu/plosonepst130/ (2_geneid_predicted.fasta). Amino acid sequences of 22,815 peptides predicted ab initio using geneid with parameters trained for PGTGgenes (same as supplementary material 2).

2. Mlaricis_populina.FrozenGeneCatalog_20091005.proteins.fasta.gz (16,694 seqs):
http://genome.jgi-psf.org/Mellp1/Mellp1.download.ftp.html
“Filtered Models” is the filtered set of models representing the best gene model for each locus.

3. puccinia_triticina_1-1_bbbd_race_1_1_proteins.fasta (11,630 seqs):
http://www.broadinstitute.org/annotation/genome/puccinia_group/MultiDownloads.html

4. puccinia_graminis_f._sp._tritici_2_proteins.fasta (15,979 seqs):
http://www.broadinstitute.org/annotation/genome/puccinia_group/MultiDownloads.html

5. Umaydis_valid_prot.fa (6,787 seqs):
http://mips.helmholtz-muenchen.de/genre/proj/ustilago/About/FTP_sites.html

BLASTx (1e-3)

Blastx_1.png

tBLASTn RESULTS

Blastx_2.png

BLASTp RESULTS

Blastx_3.png

BLASTn RESULTS

puccinia_vs_db_rust.png

BLASTn – DB: puccinia_graminis_tritici.FASTA

blastall -p blastn -d DBs/puccinia_graminis_tritici.fasta -i Hv701_Trans.fasta -o Outputs/puccinia_graminis_tritici_vs_Hv701_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_graminis_tritici.fasta -i Hv955_Trans.fasta -o Outputs/puccinia_graminis_tritici_vs_Hv955_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_graminis_tritici.fasta -i HvCatNor7_Trans.fasta -o Outputs/puccinia_graminis_tritici_vs_HvCatNor7_Trans.bn -e 1e-5

BLASTn – DB: puccinia_striiformis_tritici.FASTA

blastall -p blastn -d DBs/puccinia_striiformis_tritici.fasta -i Hv701_Trans.fasta -o Outputs/puccinia_striiformis_tritici_vs_Hv701_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_striiformis_tritici.fasta -i Hv955_Trans.fasta -o Outputs/puccinia_striiformis_tritici_vs_Hv955_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_striiformis_tritici.fasta -i HvCatNor7_Trans.fasta -o Outputs/puccinia_striiformis_tritici_vs_HvCatNor7_Trans.bn -e 1e-5

BLASTn – DB: puccinia_triticina_bbbd.FASTA

blastall -p blastn -d DBs/puccinia_triticina_bbbd.fasta -i Hv701_Trans.fasta -o Outputs/puccinia_triticina_bbbd_vs_Hv701_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_triticina_bbbd.fasta -i Hv955_Trans.fasta -o Outputs/puccinia_triticina_bbbd_vs_Hv955_Trans.bn -e 1e-5

blastall -p blastn -d DBs/puccinia_triticina_bbbd.fasta -i HvCatNor7_Trans.fasta -o Outputs/puccinia_triticina_bbbd_vs_HvCatNor7_Trans.bn -e 1e-5

BLASTn – DB: Mlaricis_populina.Filtered.FASTA

blastall -p blastn -d DBs/Mlaricis_populina.Filtered.fasta -i Hv701_Trans.fasta -o Outputs/Mlaricis_populina.Filtered_vs_Hv701_Trans.bn -e 1e-5

blastall -p blastn -d DBs/Mlaricis_populina.Filtered.fasta -i Hv955_Trans.fasta -o Outputs/Mlaricis_populina.Filtered_vs_Hv955_Trans.bn -e 1e-5

blastall -p blastn -d DBs/Mlaricis_populina.Filtered.fasta -i HvCatNor7_Trans.fasta -o Outputs/Mlaricis_populina.Filtered_vs_HvCatNor7_Trans.bn -e 1e-5

Other rust BLAST analysis

Rust_BLAST_Analysis.png

Fungus vs. Hemileia Vastatrix

BLASTx

Fungi Database Path: ftp://ftp.ncbi.nih.gov/refseq/release/51 (Jan 12, 2012)

Fungi Database concatenated fungi_prot.faa (from 14 fungi.*.prot.faa files) = 679346 seqs

Plant Database Path: ftp://ftp.ncbi.nih.gov/refseq/release/51 (Jan 12, 2012)

Plant Database concatenated plant_prot.faa (from 16 plant.*.prot.faa files) = 519211 seqs

e=1e-3

BLASTn

Task assigned on Tunebo Server

  • Path of DB: /data/process/DBs/fungi/fungus
  • Path of Query’s: /data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/
  • Working Path: /data/process/Roya/RawDataRoya/RNASeqBGI/Results/Paired_Assemby/
  • Outputs at: WORKING PATH/Out_fungus_vs_Hv/

Fungus_vs_Hv.png

BLASTn – DB: /data/process/DBs/fungi/fungus

blastall -p blastn -d /data/process/DBs/fungi/fungus -i Hv701_Trans.fasta -o Out_fungus_vs_Hv/fungus_vs_Hv701_Trans.bn -e 1e-5

blastall -p blastn -d /data/process/DBs/fungi/fungus -i Hv955_Trans.fasta -o Out_fungus_vs_Hv/fungus_vs_Hv955_Trans.bn -e 1e-5

blastall -p blastn -d /data/process/DBs/fungi/fungus -i HvCatNor7_Trans.fasta -o Out_fungus_vs_Hv/fungus_vs_HvCatNor7_Trans.bn -e 1e-5