Difference between revisions of "Sequence Alignments Protocol TSD"
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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 |
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 |
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− | === |
+ | === Count unique matches: example === |
head -1 m8blastpgp1200_it2e002.out |
head -1 m8blastpgp1200_it2e002.out |
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grep -n G1RUL9 m8blastpgp1200_it2e002.out |
grep -n G1RUL9 m8blastpgp1200_it2e002.out |
Revision as of 12:07, 7 May 2012
Contents
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
Count 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 Usage: 1_getUniprotIDS.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 -m mappingfile uniprot mappingfile
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
cut -f 2 psiblastBIGit10e002.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" > psiblastBIGit10e002.finpdb1 grep -P "\w{4}_" psiblastBIGit10e002.pdbmapping --only-matching | sed "s/_//" > psiblastBIGit10e002.finpdb2 cat psiblastBIGit10e002.finpdb2 psiblastBIGit10e002.finpdb1 | sort | uniq > psiblastBIGit10e002.finpdb
cut -f 2 psiblastBIGit10e-10.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" > psiblastBIGit10e-10.finpdb1 grep -P "\w{4}_" psiblastBIGit10e-10.pdbmapping --only-matching | sed "s/_//" > psiblastBIGit10e-10.finpdb2 cat psiblastBIGit10e-10.finpdb1 psiblastBIGit10e-10.finpdb2 | sort | uniq > psiblastBIGit10e-10.finpdb
cut -f 2 psiblastBIGit2e002.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" > psiblastBIGit2e002.finpdb1 grep -P "\w{4}_" psiblastBIGit2e002.pdbmapping --only-matching | sed "s/_//" > psiblastBIGit2e002.finpdb2 cat psiblastBIGit2e002.finpdb1 psiblastBIGit2e002.finpdb2 | sort | uniq > psiblastBIGit2e002.finpdb
cut -f 2 psiblastBIGit2e-10.mapped | tr '[A-Z]' '[a-z]' | sort | uniq | grep -P "\w{4}" > psiblastBIGit2e-10.finpdb1 grep -P "\w{4}_" psiblastBIGit2e-10.pdbmapping --only-matching | sed "s/_//" > psiblastBIGit2e-10.finpdb2 cat psiblastBIGit2e-10.finpdb1 psiblastBIGit2e-10.finpdb2 | sort | uniq > 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 | sed "s/\s//g" | sort | uniq > hhblits.finpdb rm -f hhbtemp hhbtemp2 # dont' have to do the special stuff here, the normal one doesn't find any because it's only on uniprot
COPS Parsing
The following script will read the COPS clusters (-c) and print out for every classification the members of the cluster that one or several IDs of interest (-i) are contained in. Additionally, if given a list of hits (-hi), it will count the number of hits that fall in the according cluster and the ones that don't and print out that information to a file for plotting e.g. with R. Note that you can ignore chains with the '-nc' option.
Also be aware that ignoring chains might lead to a merge of clusters. That is if given xxxx als protein of interest and xxxx,A as well was xxxx,B are contained in COPS, the final cluster which is used to calculate how many hits fall into it, will be a combination of the cluster from xxxx,A and the one from xxxx,B. That of course might be overestimating the number of hits that fall into a cluster.
Sample call: ./parseCOPSClusters.pl -c ~/Desktop/COPS-ChainHierarchy.txt -i ./interestIds -nc -hi ./union.finpdb
#!/usr/bin/env perl use strict; use warnings; use sigtrap; use autodie; use diagnostics; use Pod::Usage; use Getopt::Long qw(:config require_order); use 5.010; #For smart match, which makes this script unbelievably slow, but I'm lazy :) ##Program variables my %clusters; my @clusterOrder; my @interestIDs = (); my %interestIDLocations; my @hitsIDs = (); ##Argument my $copsPath = '/mnt/project/pracstrucfunc12/data/COPS/COPS-ChainHierarchy.txt'; my $nochain = 0; my $interestPath = './interestIds'; my $hitsPath = './union.finpdb'; ######################## ###Argument Handling#### ######################## my $result = GetOptions( 'help|h|?' => sub { pod2usage( -verbose => 1 ); }, 'man|m' => sub { pod2usage( -verbose => 2 ); }, 'c|cops=s' => \$copsPath, 'nc|nocain' => \$nochain, 'i|interest=s' => \$interestPath, 'hi|hits=s' => \$hitsPath ) or pod2usage( -verbose => 1 ) && exit; #Read IDs to look out for my $fhi; open( $fhi, '<', $interestPath ); while ( my $line = <$fhi> ) { if ( $line =~ m/(\w{4},\w)/ || $line =~ m/(\w{4})/ ) { my $iid = lc($1); push( @interestIDs, $iid ); $interestIDLocations{$iid} = {}; } } close($fhi); #Read ids that were found by prediction method(s) my $fhh; open($fhh, '<', $hitsPath); while(my $line =<$fhh>) { if($line =~ m/^(\w{4})$/) { push(@hitsIDs, lc($1)); } } close($fhh); print "Found # hits: " . scalar(@hitsIDs) . "\n"; #Parse the COPS structure my $fh; open( $fh, '<', $copsPath ); while ( my $line = <$fh> ) { if ( $line =~ m/^Chain (.+)$/ ) { #Header line found. Inititialize the cluster hash my @matches = $1 =~ m/\w+/g; for my $clusterName (@matches) { $clusters{$clusterName} = {}; } @clusterOrder = @matches; } elsif ( $line =~ m/\w{4},/ ) { #Cluster info line my @matches = $line =~ m/(\w{4},\w)/g; my $currentId = shift(@matches); # print "current id is $currentId\n"; $currentId = sanitizePdbIDs($currentId); my $count = 0; for my $representative (@matches) { $representative = sanitizePdbIDs($representative); my $currentCluster = $clusterOrder[ $count++ ]; # print "currentCluster is $currentCluster\n"; if ( !exists $clusters{$currentCluster} || !defined $clusters{$currentCluster} ) { print "this should not have happened :)\n"; next; } if ( !exists $clusters{$currentCluster}{$representative} ) { #Inititialize the cluster with the representative $clusters{$currentCluster}{$representative} = [$representative]; } #Add the current pdb id if ( !( $currentId ~~ @{ $clusters{$currentCluster}{$representative} } ) ) { #This case can only occur when we do not use the chains push( @{ $clusters{$currentCluster}{$representative} }, $currentId ); } if ( $currentId ~~ @interestIDs ) { if(!defined $interestIDLocations{$currentId}{$currentCluster}) { $interestIDLocations{$currentId}{$currentCluster}= (); } push(@{$interestIDLocations{$currentId}{$currentCluster} }, $representative); } } } } close($fh); #Do some maybe interesting output for my $intId (@interestIDs) { printClustersForId($intId); } sub printClustersForId { my $id = shift; my @allIn = (); my @allOut = (); for my $cluster ( sort(keys( $interestIDLocations{$id} ) ) ) { my %clusterMembersMerged = (); print "MEMBERS: $id -- $cluster : "; my @currentRepresentatives = @{$interestIDLocations{$id}{$cluster}}; for my $currentRepresentative (@currentRepresentatives) { my @clusterMembers = @{ $clusters{$cluster}{$currentRepresentative} }; for my $member (@clusterMembers) { # print "$member "; $clusterMembersMerged{$member} = ; } # print "\n"; } my @clusterMembersMergedArr= keys(%clusterMembersMerged); for my $e (@clusterMembersMergedArr) { print $e." "; } print "\n"; my $hitsIn = 0; my $hitsOut = 0; print "OVERLAPS: $id -- $cluster : "; for my $hit (@hitsIDs) { if($hit ~~ @clusterMembersMergedArr) { $hitsIn++; } else { $hitsOut++; } } print "In: $hitsIn, Out: $hitsOut\n"; push(@allIn, $hitsIn); push(@allOut, $hitsOut); } #Write Out In/Out over Cluster stats for plotting in R my $fho; open($fho, '>', "stats$id.plotme"); for my $cluster (sort (keys( $interestIDLocations{$id}))) { print $fho "\t$cluster"; } print $fho "\n"; print $fho "IN"; for my $elem (@allIn) { print $fho "\t$elem"; } print $fho "\n"; print $fho "OUT"; for my $elem (@allOut) { print $fho "\t$elem"; } print $fho "\n"; close($fho); } sub sanitizePdbIDs { my $id = shift; if ($nochain) { $id = substr( $id, 0, 4, ); } return $id; }
Plotting
Distribution of hits that full in and out of clusters
library(gplots) #Needs caTools, bitops and a few more. Gives us: barplot2 cbarnames <- 2.5 clwd <- 5 clwdaxis <- 20 ccaxis <- 2 maindat <- read.table('stats2gjx.plotme') mainmat <- as.matrix(maindat, header=TRUE) lab <- c("IN", "OUT") lab <- row.names(mainmat) len <- length(lab) method_col <- c("red", "blue") png("./tsd_inoutdistri.png", height=800, width=800) # par(xpd=T, mar=par()$mar+c(0,0,0,13)) barplot2(mainmat, beside=TRUE, col=method_col, cex.axis=ccaxis, cex.names=cbarnames, xpd=F, plot.ci=FALSE,cex.main=cbarnames, main="Overlap of union PDB hits with COPS Clusters") #names.arg=c("IN","OUT","IN","OUT","IN","OUT","IN","OUT","IN","OUT") legend(4,70, lab, fill=method_col, cex=2, ncol=1) par(mar=c(5, 4, 4, 2) + 0.1) # Restore default clipping rect dev.off()
Overlap of PDB hits found by the different methods
library("VennDiagram") main1<-"Overlap of PDB hits" sub1<-"BIG database" hhb <- read.table("data/hhblits.finpdb") psiit10e002 <- read.table("data/psiblastBIGit10e002.finpdb") psiit10e10<-read.table("data/psiblastBIGit10e-10.finpdb") psiit2e002<-read.table("data/psiblastBIGit2e002.finpdb") # psiit2e10<-read.table("data/psiblastBIGit2e-10.finpdb") psi=list("HHblits"=hhb[,1], "It10, Ev10e-10"=psiit10e10[,1],"It10, Ev002"=psiit10e002[,1],"It2, Ev10e-10/Ev002"=psiit2e002[,1]) venn.diagram(psi,"pdbHitsOverlap.tif", scaled = TRUE,col=c("darkblue", "darkgreen", "orange","darkorchid4"), fill=c("cornflowerblue", "green", "yellow","darkorchid1"), fontfamily = "serif", fontface = "bold", cat.col = c("darkblue", "darkgreen", "orange","darkorchid4"),cat.cex = 1.5, cat.pos = 0, cat.fontfamily = "serif", rotation.degree = 200, main=main1, sub=sub1,main.cex=2,sub.cex=1.3,lwd=1,euler.d=2,lty=1, cat.dist=c(0.1,0.1,0.13,0.1))
e-Value and identity distributions
ccmain <- 1.7 ccaxis <- 2 cclab <- 2 col1 <- "#0000ff" col2 <- "#ff0000" col3 <- "#00ff00" col4 <- "#808080" col1t <- "#0000FF80" col2t <- "#FF000080" col3t <- "#00ff0080" col4t <- "#80808080" ###Blast d <- read.table("./temp/blastall1200_IdEvfixed.plot") d_id <- d$V1 d_ev <- d$V2 #Plot identities png(width=600, height=600, "tsd_blastallIdent.png") par(mar=par()$mar+c(0,1,-1,0)) hist(d_id, breaks=100,xlim=c(0,100), main="Blast - Histogram of identities",xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1) dev.off() #Plot evalues png(width=600, height=600, "tsd_blastallEval.png") par(mar=par()$mar+c(0,1,-1,0)) hist(log(d_ev), breaks=100, main="Blast - Histogram of eValue distribution",xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1) dev.off() ###Psi-Blast normal # #Iterations e0002 # d1 <- read.table("./temp/blastpgp1200_it10e002_IdEvfixed.plot") # d2 <- read.table("./temp/blastpgp1200_it2e002_IdEvfixed.plot") # # d1_id <- d1$V1 # d1_ev <- d1$V2 # d2_id <- d2$V1 # d2_ev <- d2$V2 # # # lab = c("2 iterations", "10 iterations") # # png(width=600, height=600, "tsd_psiblastEvals_Iterations_e002.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(log(d1_ev), breaks=100,xlim=c(-430,0), ylim=c(0,70), main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 0.002, BIG80 database", cex=1.4) # hist(log(d2_ev), breaks=100,xlim=c(-430,0) ,ylim=c(0,70), col=col2t, add=T) # legend("topleft", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # png(width=600, height=600, "tsd_psiblastIdent_Iterations_e002.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(d1_id, breaks=100, xlim=c(0,160),ylim=c(0,200), main="PSI-Blast - Histogram of identities ", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 0.002, BIG80 database", cex=1.4) # hist(d2_id, breaks=100,ylim=c(0,160), col=col2t, add=T) # legend("topright", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # #Iterations 10e-10 # d1 <- read.table("./temp/blastpgp1200_it10e-10_IdEvfixed.plot") # d2 <- read.table("./temp/blastpgp1200_it2e-10_IdEvfixed.plot") # # d1_id <- d1$V1 # d1_ev <- d1$V2 # d2_id <- d2$V1 # d2_ev <- d2$V2 # # lab = c("2 iterations", "10 iterations") # # png("tsd_psiblastEvals_Iterations_10e-10.png", width=600, height=600) # par(mar=par()$mar+c(0,1,0,0)) # hist(log(d1_ev), breaks=100, ylim=c(0,70), xlim=c(-430,0) ,main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 10e-10, BIG80 database", cex=1.4) # hist(log(d2_ev), breaks=100, ylim=c(0,70),xlim=c(-430,0) ,col=col2t, add=T) # legend("topleft", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # png(width=600, height=600, "tsd_psiblastIdent_Iterations_10e-10.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(d1_id, breaks=100, xlim=c(0,100), ylim=c(0,180), main="PSI-Blast - Histogram of identities ", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 10e-10, BIG80 database", cex=1.4) # hist(d2_id, breaks=100, col=col2t, ylim=c(0,180),add=T) # legend("topright", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() d1 <- read.table("./temp/blastpgp1200_it2e002_IdEvfixed.plot") d2 <- read.table("./temp/blastpgp1200_it10e002_IdEvfixed.plot") d3 <- read.table("./temp/blastpgp1200_it2e-10_IdEvfixed.plot") d4 <- read.table("./temp/blastpgp1200_it10e-10_IdEvfixed.plot") d1_id <- d1$V1 d1_ev <- d1$V2 d2_id <- d2$V1 d2_ev <- d2$V2 d3_id <- d3$V1 d3_ev <- d3$V2 d4_id <- d4$V1 d4_ev <- d4$V2 lab = c("2 iterations, e002", "10 iterations, e002", "2 Iterations, 10e-10", "10 Iterations, 10e-10") br <- seq(-450,0,5) png("tsd_psiblastEvals_allfour.png", width=600, height=600) par(mar=par()$mar+c(0,1,0,0)) hist(log(d1_ev), breaks=br, ylim=c(0,70), xlim=c(-450,0) ,main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) mtext("BIG80 database", cex=1.4) hist(log(d2_ev), breaks=br, ylim=c(0,70),xlim=c(-450,0) ,col=col2t, add=T) hist(log(d3_ev), breaks=br, ylim=c(0,70),xlim=c(-450,0) ,col=col3t, add=T) hist(log(d4_ev), breaks=br, ylim=c(0,70),xlim=c(-450,0) ,col=col4t, add=T) legend("topright", lab, fill=c(col1t, col2t, col3t, col4t), cex=1.6, ncol=1) dev.off() lab = c("2 iterations, e002", "10 iterations, e002", "2 Iterations, 10e-10", "10 Iterations, 10e-10") br <- seq(0,100,2.5) png("tsd_psiblastIdents_allfour.png", width=600, height=600) par(mar=par()$mar+c(0,1,0,0)) hist(d1_id, breaks=br , ylim=c(0,400),main="PSI-Blast - Histogram of identities", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) mtext("BIG80 database", cex=1.4) hist(d2_id, breaks=br,col=col2t, add=T) hist(d3_id, breaks=br, col=col3t, add=T) hist(d4_id, breaks=br, col=col4t, add=T) legend("topright", lab, fill=c(col1t, col2t, col3t, col4t), cex=1.6, ncol=1) dev.off() ###PSI-Blast BIG d1 <- read.table("./temp/blastpgpBIG_3800_it2e002_IdEvfixed.plot") d2 <- read.table("./temp/blastpgpBIG_3800_it10e002_IdEvfixed.plot") d3 <- read.table("./temp/blastpgpBIG_3800_it2e-10_IdEvfixed.plot") d4 <- read.table("./temp/blastpgpBIG_3800_it10e-10_IdEvfixed.plot") d1_id <- d1$V1 d1_ev <- d1$V2 d2_id <- d2$V1 d2_ev <- d2$V2 d3_id <- d3$V1 d3_ev <- d3$V2 d4_id <- d4$V1 d4_ev <- d4$V2 lab = c("2 iterations, e002", "10 iterations, e002", "2 Iterations, 10e-10", "10 Iterations, 10e-10") br <- seq(-450,0,5) png("tsd_psiblastBIGEvals_allfour.png", width=600, height=600) par(mar=par()$mar+c(0,1,0,0)) hist(log(d1_ev), breaks=br, ylim=c(0,260), xlim=c(-450,0) ,main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) mtext("BIG database", cex=1.4) hist(log(d2_ev), breaks=br, ylim=c(0,260),xlim=c(-450,0) ,col=col2t, add=T) hist(log(d3_ev), breaks=br, ylim=c(0,260),xlim=c(-450,0) ,col=col3t, add=T) hist(log(d4_ev), breaks=br, ylim=c(0,260),xlim=c(-450,0) ,col=col4t, add=T) legend("topleft", lab, fill=c(col1t, col2t, col3t, col4t), cex=1.6, ncol=1) dev.off() lab = c("2 iterations, e002", "10 iterations, e002", "2 Iterations, 10e-10", "10 Iterations, 10e-10") br <- seq(0,100,2.5) png("tsd_psiblastBIGIdents_allfour.png", width=600, height=600) par(mar=par()$mar+c(0,1,0,0)) hist(d1_id, breaks=br , ylim=c(0,1100),main="PSI-Blast - Histogram of identities", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) mtext("BIG database", cex=1.4) hist(d2_id, breaks=br,col=col2t, add=T) hist(d3_id, breaks=br, col=col3t, add=T) hist(d4_id, breaks=br, col=col4t, add=T) legend("topright", lab, fill=c(col1t, col2t, col3t, col4t), cex=1.6, ncol=1) dev.off() # #Iterations e0002 # d1 <- read.table("./temp/blastpgpBIG_3800_it10e002_IdEvfixed.plot") # d2 <- read.table("./temp/blastpgpBIG_3800_it2e002_IdEvfixed.plot") # # d1_id <- d1$V1 # d1_ev <- d1$V2 # d2_id <- d2$V1 # d2_ev <- d2$V2 # # # lab = c("2 iterations", "10 iterations") # # png(width=600, height=600, "tsd_psiblastBIGEvals_Iterations_e002.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(log(d1_ev), breaks=100, xlim=c(-430,0) ,ylim=c(0,200),main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 0.002, BIG database", cex=1.4) # hist(log(d2_ev), breaks=100, xlim=c(-430,0) ,ylim=c(0,200),col=col2t, add=T) # legend("topleft", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # png(width=600, height=600, "tsd_psiblastBIGIdent_Iterations_e002.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(d1_id, breaks=100, xlim=c(0,100), ylim=c(0,430), main="PSI-Blast - Histogram of identities ", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 0.002, BIG database", cex=1.4) # hist(d2_id, breaks=100, col=col2t,ylim=c(0,430), add=T) # legend("topright", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # #Iterations 10e-10 # d1 <- read.table("./temp/blastpgpBIG_3800_it10e-10_IdEvfixed.plot") # d2 <- read.table("./temp/blastpgpBIG_3800_it2e-10_IdEvfixed.plot") # # d1_id <- d1$V1 # d1_ev <- d1$V2 # d2_id <- d2$V1 # d2_ev <- d2$V2 # # lab = c("2 iterations", "10 iterations") # # png(width=600, height=600, "tsd_psiblastBIGEvals_Iterations_10e-10.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(log(d1_ev), breaks=100, xlim=c(-430,0) ,ylim=c(0,280),main="PSI-Blast - Histogram of eValue distributions", xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 10e-10, BIG database", cex=1.4) # hist(log(d2_ev), breaks=100, xlim=c(-430,0), ylim=c(0,280),col=col2t, add=T) # legend("topleft", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() # # png(width=600, height=600, "tsd_psiblastBIGIdent_Iterations_10e-10.png") # par(mar=par()$mar+c(0,1,0,0)) # hist(d1_id, breaks=100, xlim=c(0,100),ylim=c(0,400), main="PSI-Blast - Histogram of identities ", xlab="% sequence identity in Blast alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1t) # mtext("Profile inclusion threshold 10e-10, BIG database", cex=1.4) # hist(d2_id, breaks=100, col=col2t, ylim=c(0,400),add=T) # legend("topright", lab, fill=c(col1t, col2t), cex=1.6, ncol=1) # dev.off() ###Hblits d <- read.table("./temp/hhblits_460_P06865_IdEvfixed.plot") d_id <- d$V1 d_ev <- d$V2 #Plot identities png(width=600, height=600, "tsd_hhblitsIdent.png") par(mar=par()$mar+c(0,1,-1,0)) hist(d_id, breaks=100, xlim=c(0,100), main="HHblits - Histogram of identities",xlab="% sequence identity in HHblits alignment", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1) dev.off() #Plot evalues png(width=600, height=600, "tsd_hhblitsEval.png") par(mar=par()$mar+c(0,1,-1,0)) hist(log(d_ev), breaks=100, main="HHblits - Histogram of eValue distribution",xlab="log(eValue)", cex.axis=ccaxis, cex.main=ccmain, cex.lab=cclab, col=col1) dev.off()
MSA
Dataset creation
# Get details for the pdb proteins union grep -f pdbSets/union.finpdb m8blastpgpBIG_3800*.out > pdbunionBlast
Runs
p="/mnt/home/student/meiera/1_SeqAli/2_MSA" export PATH=$PATH:/mnt/opt/T-Coffee/bin/
clustalw -align -infile=$p/datasets/msaset_40.fasta -outfile=$p/clustalw_msaset_40.aln clustalw -align -infile=$p/datasets/msaset_60.fasta -outfile=$p/clustalw_msaset_60.aln clustalw -align -infile=$p/datasets/msaset_all.fasta -outfile=$p/clustalw_msaset_all.aln clustalw -infile=$p/datasets/msaset_40.fasta -outfile=$p/clustalw_TESTmsaset_40.aln
muscle -in $p/datasets/msaset_40.fasta -out $p/muscle_msaset_40.msa -quiet muscle -in $p/datasets/msaset_60.fasta -out $p/muscle_msaset_60.msa -quiet muscle -in $p/datasets/msaset_all.fasta -out $p/muscle_msaset_all.msa -quiet
t_coffee $p/datasets/msaset_40.fasta -outfile tcdef_40.aln t_coffee $p/datasets/msaset_60.fasta -outfile tcdef_60.aln t_coffee $p/datasets/msaset_all.fasta -outfile tcdef_all.aln
t_coffee $p/datasets/msaset_40.fasta -method sap_pair -template_file 3nsn_A -outfile tc3d_40.aln t_coffee $p/datasets/msaset_60.fasta -method sap_pair -template_file 2gjx_A -outfile tc3d_60.aln t_coffee $p/datasets/msaset_all.fasta -method sap_pair -template_file 3lmy_A -outfile tc3d_all.aln