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
1. Hv701_Trans.fasta vs nr
2. Hv955_Trans.fasta Vs Nr
3. HvCatNor7_Trans.fasta vs Nr
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)
tBLASTn RESULTS
BLASTp RESULTS
BLASTn RESULTS
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
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/
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