Difference between revisions of "Sequence Alignments Protocol TSD"

From Bioinformatikpedia
(Sequence identity and e-values)
(Unique identifiers for Blast and HHblits)
Line 51: Line 51:
 
=== Unique identifiers for Blast and HHblits ===
 
=== Unique identifiers for Blast and HHblits ===
 
/mnt/home/student/meiera/bin/1_forPdbMapping.pl
 
/mnt/home/student/meiera/bin/1_forPdbMapping.pl
  +
Usage: 1_forPdbMapping.pl [flags] file...
  +
flags:
  +
-i Infile reads the input from fileIN
  +
-o OutFile writes uniprot identifiers to fileOUT
  +
-h = hhblits input, default is set to blastoutput
  +
 
 
 
#Use uniprot.org's online mapping service on the .pdbmapping files and save the results to .mapped files
 
#Use uniprot.org's online mapping service on the .pdbmapping files and save the results to .mapped files

Revision as of 14:37, 5 May 2012

Blast

blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -b 1200 -v 1200 > /mnt/home/student/meiera /1_SeqAli/1_SeqSearch/blastall_1200alis.out

PSI-Blast

Big80

time blastpgp -C blastpgp1200_pssmdefault -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -v 1200 -b 1200 > /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/blastpgp1200_default.out
time blastpgp -C blastpgp1200_pssmit2e002 -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -j 2 -h "0.002" -v 1200 -b 1200 >  /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/blastpgp1200_it2e002.out
time blastpgp -C blastpgp1200_pssmit10e002 -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -j 10 -h "0.002" -v 1200 -b 1200 >  /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/blastpgp1200_it10e002.out
time blastpgp -C blastpgp1200_pssmit10e-10 -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -j 10 -h "10E-10" -v 1200 -b 1200 >  /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/blastpgp1200_it10e-10.out
time blastpgp -C blastpgp1200_pssmit2e-10 -d /mnt/project/pracstrucfunc12/data/big/big_80 -i /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/P06865.fasta -j 2 -h "10E-10" -v 1200 -b 1200 >  /mnt/home/student/meiera/1_SeqAli/1_SeqSearch/blastpgp1200_it2e-10.out

Big

PAT="/mnt/home/student/meiera/1_SeqAli/1_SeqSearch"
time blastpgp -R $PAT/blastpgp1200_pssmit2e002 -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 > $PAT/blastpgpBIG_3800_it2e002.out
time blastpgp -R $PAT/blastpgp1200_pssmit10e002 -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 > $PAT/blastpgpBIG_3800_it10e002.out
time blastpgp -R $PAT/blastpgp1200_pssmit2e-10 -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 > $PAT/blastpgpBIG_3800_it2e-10.out
time blastpgp -R $PAT/blastpgp1200_pssmit10e-10 -d /mnt/project/pracstrucfunc12/data/big/big -i $PAT/P06865.fasta -v 3800 -b 3800 > $PAT/blastpgpBIG_3800_it10e-10.out

Find Unique matches: example

head -1 m8blastpgp1200_it2e002.out
grep -n G1RUL9 m8blastpgp1200_it2e002.out
tail -n +1233 m8blastpgp1200_it2e002.out | cut -f 2 | wc -l
tail -n +1233 m8blastpgp1200_it2e002.out | uniq -w 44 | wc -l

HHblits

WD="/mnt/home/student/meiera/1_SeqAli/1_SeqSearch"
time hhblits -i $WD/P06865.fasta -o $WD/hhblits_460_P06865.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -Z 460 -B 460 > $WD/hhblits_460_P06865_stdout.log
time hhblits -i $WD/P06865.fasta -n 10 -o $WD/hhblits_460_P06865_10it.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -Z 460 -B 460 > $WD/hhblits_460_P06865_10_stdout.log
time hhblits -i $WD/P06865.fasta -n 10 -o $WD/hhblits_2500_P06865_10it.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -Z 2500 -B 2500 > $WD/hhblits_2500_P06865_10_stdout.log
time hhblits -i $WD/P06865.fasta -n 2 -o $WD/hhblits_460_P06865_2it.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -Z 460 -B 460 > $WD/hhblits_460_P06865_2_stdout.log
time hhblits -i $WD/P06865.fasta -n 2 -o $WD/hhblits_2500_P06865_2it.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -Z 2500 -B 2500 > $WD/hhblits_2500_P06865_2_stdout.log
time hhsearch -i $WD/P06865.fasta -o $WD/hhblits_460_P06865.hhr -d /mnt/project/pracstrucfunc12/data/hhblits/pdb70_current_hhm_db -Z 14 -B 14 > $WD/hhblits_pdb_1500_P06865_stdout.log


Preparation of outputs

Sequence identity and e-values

#for both Blast and HHblits output
/mnt/home/student/meiera/bin/1_parseidentity.pl
Usage: 1_parseidentity.pl [flags] file...
flags:
   -i Infile   reads the input from fileIN 
   -o OutFile  writes output to fileOUT 
   -h	Input is hhblits, default is blast

Uniprot sets for Venn diagrams

#for both Blast and HHblits output, also computation of the unique ids for HHblits
 /mnt/home/student/meiera/bin/1_getUniprotIDS.pl 

Build PDB sets

Unique identifiers for Blast and HHblits

/mnt/home/student/meiera/bin/1_forPdbMapping.pl
Usage: 1_forPdbMapping.pl [flags] file...
flags:
   -i Infile   reads the input from fileIN 
   -o OutFile  writes uniprot identifiers to fileOUT 
   -h = hhblits input, default is set to blastoutput


#Use uniprot.org's online mapping service on the .pdbmapping files and save the results to .mapped files
#Create sets with unique ids, ignoring chains
cut -f 2 psiblastBIGit10e002.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" >  psiblastBIGit10e002.finpdb
cut -f 2  psiblastBIGit10e-10.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" >   psiblastBIGit10e-10.finpdb
cut -f 2 psiblastBIGit2e002.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" >  psiblastBIGit2e002.finpdb
cut -f 2 psiblastBIGit2e-10.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" >  psiblastBIGit2e-10.finpdb
cut -f 2 hhblits__460.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" > hhbtemp
sed "s/_\w//g" hhblits_pdb_1500.pdbmapping > hhbtemp2
cat hhbtemp hhbtemp2 | sort | uniq > hhblits.finpdb
rm -f hhbtemp hhbtemp2