Commit 0f5b7d2b authored by Aroon Chande's avatar Aroon Chande

WWW files

parents
File added
# Files for vibriocholera.com
## www
Files for the main website
## t6ss
Files for the T6ES prediction tool.
Perl script placeholders, actual scripts are available on request
File added
<!-- Footer -->
<hr>
<footer id="footer">
<div class="alert alert-success">
<strong>To cite : </strong> Chande et al. 2016. Computational characterization of Type VI Secretion Systems in <i>Vibrio cholerae</i> (Manuscript in preparation)<br/>
</div>
</footer>
<!DOCTYPE html>
<html lang="en">
<h3>Predict Type VI Secretion System Loci and Proteins</h3>
<div class="row">
<div class="col-md-8">
<p>Type VI Secretion Systems (T6SS) are bacterial weaponry designed to poison, and potentially kill, neighboring bacteria and eukaryotic cells. T6SS relies on a set of structural proteins, encoded in what's called the Large Cluster, and a set of effector/immunity pairs encoded on Auxiliary clusters. This tool attempts to predict Auxiliary Cluster loci and their VgrG (required, "spike" protein) and Effector (toxin)</p>
<div class="col-md-6">
<img class="img-responsive" src='t6loci.png'/>
</div>
</div>
</html>
library('shiny')
library('genoPlotR')
t6pred <- function(outdir){
annotate <- paste('/home/blast/prediction_server/server/predict_t6.pl -fasta ',outdir,'/prots.faa', sep="")
system(annotate)
}
plotGff <- function(outdir){
genplotdata <-
paste(
'/home/blast/prediction_server/server/gff.pl -fasta '
,outdir,'/prots.faa', sep="")
system(genplotdata)
filelist = dir(outdir, pattern = "*.ptt")
dna <- list()
annot <- list()
for (i in 1:length(filelist)) {
file = paste(outdir, filelist[i], sep = "")
dna[[i]] <- read_dna_seg_from_ptt(file)
mid_pos <- middle(dna[[i]])
annot[[i]] <-
annotation(x1 = mid_pos,
text = dna[[i]]$name,
rot = "45")
}
plot_gene_map(dna_segs = dna, annotations = annot)
}
plotSkel <- function(outdir){
genplotdata <-
paste(
'/home/blast/prediction_server/server/gff.pl -fasta '
,outdir,'/prots.faa', sep="")
system(genplotdata)
filelist = dir(outdir, pattern = "*.ptt")
dna <- list()
annot <- list()
for (i in 1:length(filelist)) {
file = paste(outdir, filelist[i], sep = "")
dna[[i]] <- read_dna_seg_from_ptt(file)
mid_pos <- middle(dna[[i]])
annot[[i]] <-
annotation(x1 = mid_pos,
text = dna[[i]]$name,
rot = "45")
}
plot_gene_map(dna_segs = dna, annotations = annot)
}
shinyServer(function(input, output, session) {
observe({
# switch tab
if (!is.null(input$fastaFile) & input$submit != 0L) {
updateTabsetPanel(session, "vchot6ss", selected = "T6SS Predictions")
}
})
annotPlot = reactive({
seqCond = input$seqType
predCond = input$predict
if (seqCond == 'protein' &
predCond == 'pred' &
input$submit != 0L & !is.null(input$fastaFile)) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) - 1)
cpProt <- paste('cp ', input$fastaFile$datapath, ' ', outdir, '/prots.faa', sep="")
system(cpProt)
sed <- paste("sed -i 's/ #.*.//g' ",outdir,"/prots.faa", sep="")
system(sed)
t6pred(outdir)
}
else if (predCond == 'pred' &
seqCond == 'genomic' &
input$submit != 0L & !is.null(input$fastaFile)) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) - 1)
prediction <- paste('prodigal -q -c -i ', input$fastaFile$datapath, ' -a ', outdir, '/prots.faa -f gff -o ',outdir,'/prots.gff 2> /dev/null', sep="")
system(prediction)
sed <- paste("sed -i 's/ #.*.//g' ",outdir,"/prots.faa", sep="")
system(sed)
t6pred(outdir)
plotGff(outdir)
}
else if (predCond == 'nopred' &
seqCond == 'genomic' &
input$submit != 0L & !is.null(input$fastaFile) & !is.null(input$gffFile)) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) - 1)
prediction <- paste('prodigal -q -c -i ', input$fastaFile$datapath, ' -a ', outdir, '/prots.faa -f gff -o ',outdir,'/prots.gff 2> /dev/null', sep="")
}
# else if (predCond == 'nopred' &
# input$submit != 0L &
# !is.null(input$fastaFile) & !is.null(input$gffFile)) {
# outdir = substr(input$fastaFile$datapath,
# 1,
# nchar(input$fastaFile$datapath) - 1)
# annotate <-
# paste(
# '/home/blast/prediction_server/server/predict_t6.pl -predict no -fasta ',
# input$fastaFile$datapath,
# ' -gff ',
# input$gffFile$datapath
# )
# #system('echo "',input$fastaFile$datapath,'\n$(date) >> ~/vibrio_project/webtest.txt"', intern = TRUE)
# system(annotate)
# genplotdata <-
# paste(
# '/home/blast/prediction_server/server/gff.pl -fasta ',
# input$fastaFile$datapath
# )
# system(genplotdata)
# filelist = dir(outdir, pattern = "*.ptt")
# dna <- list()
# annot <- list()
# for (i in 1:length(filelist)) {
# file = paste(outdir, filelist[i], sep = "")
# dna[[i]] <- read_dna_seg_from_ptt(file)
# mid_pos <- middle(dna[[i]])
# annot[[i]] <-
# annotation(x1 = mid_pos,
# text = dna[[i]]$name,
# rot = "45")
# }
#
# plot_gene_map(dna_segs = dna, annotations = annot)
# }
else{
return(NULL)
}
})
output$plot = renderPlot({
annotPlot()
})
output$dlFasta = downloadHandler(
filename = function() {
paste("proteins",
paste(collapse = '-'),
'-',
gsub(' ', '-', gsub(':', '-', Sys.time())),
'.faa',
sep = '')
},
content = function(file) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) -
1)
copyFile = paste(outdir, "prots.faa", sep = "")
file.copy(copyFile, file)
}
)
output$dlPreds = downloadHandler(
filename = function() {
paste("predictions",
paste(collapse = '-'),
'-',
gsub(' ', '-', gsub(':', '-', Sys.time())),
'.faa',
sep = '')
},
content = function(file) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) -
1)
copyFile = paste(outdir, "predictions.faa", sep = "")
file.copy(copyFile, file)
}
)
})
library('shiny')
library('genoPlotR')
# actionButton with dark color
nx.actionButton = function (inputId, label, icon = NULL) {
if (!is.null(icon))
buttonContent <- list(icon, label)
else
buttonContent <- label
tags$button(id = inputId,
type = "button",
class = "btn btn-primary action-button",
buttonContent)
}
shinyUI(
fluidPage(
theme = 'cerulean.css',
tags$head(includeScript("www/ga.js")),
headerPanel(title = "T6SS Predictor", windowTitle = 'Predict T6SS Proteins'),
sidebarPanel(
radioButtons(
"seqType",
"1. Are you providing a genome sequence (FASTA nucleotide) or predicted proteins (FASTA amino acid)?",
c("Proteins (faa)" = "protein",
"Genome (fna)" = "genomic")
),
strong("2."),
#br(),
fileInput('fastaFile', 'Upload FASTA file'),
a('Example genome sequence file', href='bgt8_genomic.fna'),
br(),
a('Example protein sequence file', href='bgt8_cds.faa'),
br(),
conditionalPanel(
condition = "input.seqType == 'protein'",
strong("3. Click the button and be patient. Predictions take ~5 mins"),
hr()
),
conditionalPanel(
radioButtons(
"predict",
"3. Are you providing your own annotation (GFF)?",
c("No" = "pred",
"Yes" = "nopred")
),
condition = "input.seqType == 'genomic'",
conditionalPanel(
condition = "input.predict == 'pred'",
strong("4. Click the button and be patient. Predictions take ~5 mins"),
hr()
),
conditionalPanel(
condition = "input.predict == 'nopred'",
strong('4. Upload your GFF file'),
fileInput('gffFile', 'Upload GFF file'),
a('Example GFF file', href='bgt8.gff'),
br(),
strong("5. Click the button and be patient. Predictions take ~5 mins"),
hr()
)),
nx.actionButton('submit', 'Predict T6SS'),
tags$hr()
),
mainPanel(# css hack to move the progress bar to a lower place
# from https://gist.github.com/johndharrison/9578241
# tags$link(rel = 'stylesheet', type = 'text/css', href = 'progbar.css'),
tabsetPanel(
id = 'vchot6ss',
tabPanel(
"Introduction",
p(
"Type VI Secretion Systems (T6SS) are bacterial weaponry designed to poison, and potentially kill, neighboring bacteria and eukaryotic cells. T6SS relies on a set of structural proteins, encoded in what's called the Large Cluster, and a set of effector/immunity pairs encoded on Auxiliary clusters. This tool attempts to predict Auxiliary Cluster loci and their VgrG and Effector proteins"
),
img(src = 't6loci.png', align = "center")
),
tabPanel(
"T6SS Predictions",
h3("Predicted Type VI Secretion System Loci and Proteins"),
tags$hr(),
plotOutput("plot"),
tags$hr(),
downloadButton('dlFasta', 'Download Fasta Amino Acid',
class = 'btn btn-primary btn-large'),
downloadButton('dlPreds', 'Download predicted T6SS proteins',
class = 'btn btn-primary btn-large')
)
),
includeHTML('footer.html')
)
)
)
\ No newline at end of file
This source diff could not be displayed because it is too large. You can view the blob instead.
>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE PE=1 SV=1
MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASW
RIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVF
YYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVF
YYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGE
EQNKEALQDVEDENQ
>sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH PE=1 SV=4
MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSW
RVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESK
VFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFS
VFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDE
EAGEGN
>sp|P61981|1433G_HUMAN 14-3-3 protein gamma OS=Homo sapiens GN=YWHAG PE=1 SV=2
MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSW
RVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESK
VFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYS
VFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDD
DGGEGNN
>sp|P31947|1433S_HUMAN 14-3-3 protein sigma OS=Homo sapiens GN=SFN PE=1 SV=1
MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWR
VLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFY
LKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFH
YEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGG
EAPQEPQS
>sp|P27348|1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1
MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWR
VISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLK
MKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYE
ILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAA
EGAEN
>sp|P63104|1433Z_HUMAN 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ PE=1 SV=1
MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWR
VVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLK
MKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYE
ILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAG
EGGEN
>sp|P30443|1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain OS=Homo sapiens GN=HLA-A PE=1 SV=1
MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQ
IMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQR
RVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEL
SSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSL
TACKV
>sp|P01892|1A02_HUMAN HLA class I histocompatibility antigen, A-2 alpha chain OS=Homo sapiens GN=HLA-A PE=1 SV=1
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
SSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSL
TACKV
>sp|P04439|1A03_HUMAN HLA class I histocompatibility antigen, A-3 alpha chain OS=Homo sapiens GN=HLA-A PE=1 SV=2
MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQ
IMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQL
RAYLDGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEL
SSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSL
TACKV
<!-- Footer -->
<hr>
<footer id="footer">
<div class="alert alert-success">
<strong>To cite : </strong> Chande et al. 2016. Computational characterization of Type VI Secretion Systems in <i>Vibrio cholerae</i> (Manuscript in preparation)<br/>
</div>
</footer>
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<!DOCTYPE html>
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<h3>Predict Type VI Secretion System Loci and Proteins</h3>
<div class="row">
<div class="col-md-8">
<p>Type VI Secretion Systems (T6SS) are bacterial weaponry designed to poison, and potentially kill, neighboring bacteria and eukaryotic cells. T6SS relies on a set of structural proteins, encoded in what's called the Large Cluster, and a set of effector/immunity pairs encoded on Auxiliary clusters. This tool attempts to predict Auxiliary Cluster loci and their VgrG (required, "spike" protein) and Effector (toxin)</p>
<div class="col-md-6">
<img class="img-responsive" src='t6loci.png'/>
</div>
</div>
</html>
.shiny-progress-container {
margin-top: 50px !important;
}
<html><head>
<meta name="keywords" content="V. cholerae, T6SS, gatech, hammer">
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<h1 class="text-inverse">
<i>Vibrio cholerae</i>&nbsp;research @ Hammer Lab</h1>
<p class="text-inverse">The <a href="http://www.hammerlab.biology.gatech.edu/">Hammer Lab</a> at <a href="http://www.gatech.edu">Georgia Tech</a> studies how bacteria sense and respond
to their environment. Recently we started investigating Type VI secretion
systems and how
<i>V. cholerae</i>use T6SS to invade and maintain their niche in both the
environment and in human hosts.</p>
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<h1>Type VI secretion systems</h1>
<h3>Bacterial warfare using T6SS</h3>
<p>T6SS acts like a hypodermic needle, delivering toxins across the membrane
into a neighboring cell.&nbsp;</p>
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<h2>T6SS Predictor</h2>
<p>Predict T6SS genes and loci in your strains of interest
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<a class="btn btn-default" href="https://t6ss.vibriocholera.com/">Predict your T6SS genes</a>
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<p>BLAST your favorite sequences against our samples. We use the awesome
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<div class="row"><div class="col-md-12"><hr></div></div><div class="row"><div class="col-md-12"><div class="page-header"><h2>Recent papers</h2></div></div></div><div class="row">
<div class="col-md-12"><ol><li>Bernardy EE, Turnsek MA, Wilson SK, Tarr CL, Hammer BK.2016. Diversity of Clinical and Environmental Isolates of Vibrio cholerae in Natural Transformation and Contact-Dependent Bacterial Killing Indicative of Type VI Secretion System Activity.<a href="http://www.ncbi.nlm.nih.gov/pubmed/26944842"> Appl Environ Microbiol 82(9):2833-2842.</a></li><li>Watve S, Thomas J &amp; Hammer BK. 2015. Watve SS, Thomas J, Hammer BK.2015. CytR Is a Global Positive Regulator of Competence, Type VI Secretion, and Chitinases in Vibrio cholerae. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138834">PLoS ONE 10(9):e0138834.</a></li><li>Antonova ES, Hammer BK. 2015 Genetics of Natural Competence in Vibrio cholerae and other Vibrios. <a href="http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.VE-0010-2014">Microbiol Spectrum 3(3):VE-0010-2014Three</a></li></ol></div>
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<title>Predict T6SS Proteins</title>
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