FORWARD: bin/scan_for_matches patro < genomes/M.musculus/cDNA/fantom2.00.seq.ri.fa > IRESpatroforward.txt
REVERSE: bin/scan_for_matches -c patro < genomes/M.musculus/cDNA/fantom2.00.seq.ri.fa > IRESpatroreverse.txt
[2]
IRESpatroforward.txt: grep -c \> IRESpatroforward.txt (191 IREs)
IRESpatroreverse.txt: grep -c \> IRESpatroreverse.txt (337 IREs, 146 in reverse)
IRESpatrolaxeforward.txt: grep -c \> IRESpatrolaxeforward.txt (601 IREs)
IRESpatrolaxereverse.txt: grep -c \> IRESpatrolaxereverse.txt (1124 IREs, 523 in reverse)
[3]
IRESpatroforward.txt: grep \> IRESpatroforward.txt | gawk -F":" '{print $1}' | uniq | wc -l (187 cDNAs)
IRESpatroreverse.txt: grep \> IRESpatroreverse.txt | gawk -F":" '{print $1}' | uniq | wc -l (332 cDNAs)
IRESpatrolaxeforward.txt: grep \> IRESpatrolaxeforward.txt | gawk -F":" '{print $1}' | uniq | wc -l (594 cDNAs)
IRESpatroreverse.txt: grep \> IRESpatrolaxereverse.txt | gawk -F":" '{print $1}' | uniq | wc -l (1106 cDNAs)
[4] BLAST (UNIX)
- export HUMANGENOME="chr10.fa.masked chr10_random.fa.masked chr11.fa.masked chr11_random.fa.masked chr12.fa.masked chr12_random.fa.masked chr13.fa.masked chr14.fa.masked chr14_random.fa.masked chr15.fa.masked chr15_random.fa.masked chr16.fa.masked chr16_random.fa.masked chr17.fa.masked chr17_random.fa.masked chr18.fa.masked chr19.fa.masked chr19_random.fa.masked chr1.fa.masked chr1_random.fa.masked chr20.fa.masked chr21.fa.masked chr22.fa.masked chr2.fa.masked chr2_random.fa.masked chr3.fa.masked chr3_random.fa.masked chr4.fa.masked chr4_random.fa.masked chr5.fa.masked chr6.fa.masked chr6_random.fa.masked chr7.fa.masked chr8.fa.masked chr8_random.fa.masked chr9.fa.masked chr9_random.fa.masked chrM.fa.masked chrUn_random.fa.masked chrX.fa.masked chrY.fa.masked"
- export BLASTDB="db/H.sapiens/golden_path_200211/chromFa_msk/"
- blastall -p blastn -d "$HUMANGENOME" -i IRESpatroforward.fasta -e 0.1 -o IRESpatrolaxeforward.blast
[5] BLASTMACHINE
- export PB_BLASTDB="disk1/H.sapiens/golden_path_20020628/chromosomes/
- export HUMANGENOME="chr1.fa.msk chr10.fa.msk chr11.fa.msk chr11_random.fa.msk chr12.fa.msk chr12_random.fa.msk chr13.fa.msk chr14.fa.msk chr15.fa.msk chr15_random.fa.msk chr16.fa.msk chr16_random.fa.msk chr17.fa.msk chr17_random.fa.msk chr18.fa.msk chr19.fa.msk chr19_random.fa.msk chr2.fa.msk chr20.fa.msk chr21.fa.msk chr22.fa.msk chr2_random.fa.msk chr3.fa.msk chr4.fa.msk chr4_random.fa.msk chr5.fa.msk chr6.fa.msk chr6_random.fa.msk chr7.fa.msk chr8.fa.msk chr8_random.fa.msk chr9.fa.msk chr9_random.fa.msk chrM.fa.msk chrUn_random.fa.msk chrX.fa.msk chrX_random.fa.msk chrY.fa.msk"
- pb blastall -p blastn -d "$HUMANGENOME" -i IRESpatroforward.fasta -e 0.1 -o IRESpatrolaxeforward.blast
[6] BLASTMACHINE
- export BLASTDB="db/H.sapiens/golden_path_200211/chromFa_msk/"
- Test: blastall -p blastn -d chr22.fa.masked -i IRESpatrolaxeforward.fasta -e 0.1 -o IRESpatrolaxeforward.blast (DONE)
- Loop: for name in $(cd genomes/H.sapiens/golden_path_200211/chromFa_msk/; ls -1 chr*); do cd; blastall -p blastn -i IRESpatrolaxeforward.fasta -d $name -e 0.1 -o Tblastn/$name.blastn; done
[7] BLAST (ESTs database)
nice -n 10 scan_for_matches -c patrolaxe genomes/H.sapiens/TCs/HGI.092702 > HGI.092702.IRESpatrolaxereverse
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