bch441-work-abc-units/BIN-ALI-BLAST.R

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# BIN-ALI-BLAST.R
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-BLAST unit.
#
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# Version: 1.0
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#
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# Date: 2017 10 23
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
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# 1.0 First live version 2017.
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# 0.1 First code copied from 2016 material.
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#
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#
# TODO:
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
# answer, or ask your instructor. Don't continue if you don't understand what's
# going on. That's not how it works ...
#
# ==============================================================================
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#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------
#TOC> 1 Preparations 41
#TOC> 2 Defining the APSES domain 54
#TOC> 3 Executing the BLAST search 76
#TOC> 4 Analysing results 98
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#TOC>
#TOC> ==========================================================================
# = 1 Preparations ========================================================
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if (!require(Biostrings, quietly=TRUE)) {
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
library(Biostrings)
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}
# Package information:
# library(help = Biostrings) # basic information
# browseVignettes("Biostrings") # available vignettes
# data(package = "Biostrings") # available datasets
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# = 2 Defining the APSES domain ===========================================
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# Load your protein database
source("makeProteinDB.R")
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# Get the APSES domain sequence for MBP1_MYSPE feature annotation. (You have
# entered this data in the BIN-ALI-Optimal_sequence_alignment unit.)
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(proID <- myDB$protein$ID[myDB$protein$name == "MBP1_<MYSSPE>"]) # <<< EDIT
(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
myDB$annotation$featureID == ftrID])
(start <- myDB$annotation$start[myDB$annotation$ID == fanID])
(end <- myDB$annotation$end[myDB$annotation$ID == fanID])
(apses <- substr(myDB$protein$sequence[myDB$protein$ID == proID],
start,
end))
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# The MYSPE "apses" sequence is the sequence that we will use for our reverse
# BLAST search.
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# = 3 Executing the BLAST search ==========================================
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# The ./scripts/BLAST.R code defines two functions to access the BLAST interface
# through its Web API, and to parse results. Have a look at the script, then
# source it:
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source("./scripts/BLAST.R")
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# Use BLAST() to find the best match to the MYSPE APSES domain in Saccharomyces
# cerevisiae:
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BLASThits <- BLAST(apses, # MYSPE APSES domain sequence
db = "refseq_protein", # database to search in
nHits = 10, #
E = 0.01, #
limits = "txid559292[ORGN]") # S. cerevisiae S288c
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length(BLASThits) # There should be at least one hit there. Ask for advice
# in case this step fails.
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# = 4 Analysing results ===================================================
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# The BLAST.R script has defined a convenience function to parse BLAST
# alignments.
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(topHit <- parseBLASTalignment(BLASThits, idx = 1)) # Parse the top hit
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# What is the refseq ID of the top hit
topHit$accession
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# If this is "NP_010227.1" you have confirmed the RBM of the MYSPE apses
# domain. If it is not, ask me for advice.
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# [END]