<<<< BLAST EN COMMAND LINE Y VISUALIZACION DEL ALINEAMIENTO >>>> formatdb -p F -i pRi2659_Arhizogenes.fa formatdb -p F -i pRi1724_Arhizogenes.fa formatdb -p F -i pRi8196_Arhizogenes.fa formatdb -p F -i pTiC58_Atumefaciens.fa formatdb -p F -i pRiA4_TL-DNA_Arhizogenes.fa formatdb -p F -i pTi15955_Atumefaciens.fa formatdb -p F -i Streptomyces.fa # estamos en: cd /home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO/FASTA # export PATH=$PATH:/disc8/bin/:/disc8/bin/ncbiblast/bin/:/disc8/soft/R/bin export BLASTMAT="/disc8/bin/ncbiblast/data" export BLASTMAT="/disc8/bin/blast-2.2.13/data"; --> pRi2659 ---BLO80 blastall -p tblastx -d pRi2659_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff # estamos en: cd /home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO # export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi2659.Arhizo"; print $0 } ' $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pRi2659_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi2659.Arhizo"; print $0 } ' $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pRi2659_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi2659.Arhizo"; print $0 } ' $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi2659_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> pRi1724 ---BLO80 blastall -p tblastx -d pRi1724_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi1724.Arhizo"; print $0 } ' $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vrWwI -K "R" --nopswarnings \ --x-sequence-coords 1..16500 \ --y-sequence-coords 10000..25000 -- \ $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi1724_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pRi1724_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi1724.Arhizo"; print $0 } ' $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vrWwI -K "R" --nopswarnings \ --x-sequence-coords 1..16500 \ --y-sequence-coords 10000..25000 -- \ $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi1724_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pRi1724_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi1724.Arhizo"; print $0 } ' $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vrWwI -K "R" --nopswarnings \ --x-sequence-coords 1..16500 \ --y-sequence-coords 10000..25000 -- \ $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi1724_Arhizogenes.genbank.gff \ > $BD/FASTA/pRi1724_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> pRi8196 ---BLO80 blastall -p tblastx -d pRi8196_T-DNAorf10-14_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.out \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi8196.Arhizo"; print $0 } ' $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi8196_Arhizogenes.genbank.gff \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pRi8196_T-DNAorf10-14_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi8196.Arhizo"; print $0 } ' $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi8196_Arhizogenes.genbank.gff \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pRi8196_T-DNAorf10-14_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRi8196.Arhizo"; print $0 } ' $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRi8196_Arhizogenes.genbank.gff \ > pRi8196_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> pTiC58 ---BLO80 blastall -p tblastx -d pTiC58_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.out \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTiC58.Atumefa"; print $0 } ' $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTiC58_Atumefaciens.genbank.gff \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pTiC58_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTiC58.Atumefa"; print $0 } ' $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTiC58_Atumefaciens.genbank.gff \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pTiC58_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTiC58.Atumefa"; print $0 } ' $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTiC58_Atumefacienss.genbank.gff \ > pTiC58_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> pRiA4 ---BLO80 blastall -p tblastx -d pRiA4_TL-DNA_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO80.out parseblast.pl -A -b pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO80.out \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRiA4.Arhizo"; print $0 } ' $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRiA4_Arhizogenes.genbank.gff \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pRiA4_TL-DNA_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRiA4.Arhizo"; print $0 } ' $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRiA4_Arhizogenes.genbank.gff \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pRiA4_TL-DNA_Arhizogenes.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pRiA4.Arhizo"; print $0 } ' $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pRiA4_Arhizogenes.genbank.gff \ > pRiA4_Arhizogenes-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> pTi15955 ---BLO80 blastall -p tblastx -d pTi15955_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.out \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTi15955.Atumefa"; print $0 } ' $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTi15955_Atumefaciens.genbank.gff \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d pTi15955_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTi15955.Atumefa"; print $0 } ' $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTi15955_Atumefaciens.genbank.gff \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d pTi15955_Atumefaciens.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:TDNA.pTi15955.Atumefa"; print $0 } ' $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.pTi15955_Atumefaciens.genbank.gff \ > pTi15955_Atumefaciens-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps --> Streptomyces ---BLO80 blastall -p tblastx -d Streptomyces.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM80 \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx.out parseblast.pl -A -b Streptomyces-x-pRi2659_Arhizogenes.tblastx.out \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:Streptomyces"; print $0 } ' $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx.aplot.gff \ > $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/Streptomyces.genbank.gff \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx.aplot.ps ---BLO62 blastall -p tblastx -d Streptomyces.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM62 \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.out parseblast.pl -A -b Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.out \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:Streptomyces"; print $0 } ' $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.gff \ > $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/TDNA.Streptomyces.genbank.gff \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO62.aplot.ps ---BLO45 blastall -p tblastx -d Streptomyces.fa \ -i pRi2659_Arhizogenes.fa -M BLOSUM45 \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.out parseblast.pl -A -b Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.out \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff export BD="/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO" gawk '{ $1="TDNA.pRi2659.Arhizo:Streptomyces"; print $0 } ' $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.gff \ > $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff gff2aplot.pl -vWwI --nopswarnings -K "R" -- \ $BD/FASTA/Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot_short.gff \ $BD/GenBank/TDNA.pRi2659_Arhizogenes.genbank.gff \ $BD/GenBank/Streptomyces.genbank.gff \ > Streptomyces-x-pRi2659_Arhizogenes.tblastx_BLO45.aplot.ps <<<< VISUALIZACION DE LOS fichero.ps >>>> kghostview fichero.ps <<<< CONVERSION DE LAS IMAGENES A FORMATO png >>>> convert -antialias fichero.ps fichero.png