113 lines
3.6 KiB
R
113 lines
3.6 KiB
R
# BIN-ALI-BLAST.R
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-ALI-BLAST unit.
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#
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# Version: 1.1
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#
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# Date: 2017 10 23
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.1 Fixed parsing logic.
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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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#
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# TODO:
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#
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#
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# == 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
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ---------------------------------------------
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#TOC> 1 Preparations 41
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#TOC> 2 Defining the APSES domain 54
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#TOC> 3 Executing the BLAST search 76
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#TOC> 4 Analysing results 98
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#TOC>
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#TOC> ==========================================================================
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# = 1 Preparations ========================================================
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if (!require(Biostrings, quietly=TRUE)) {
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source("https://bioconductor.org/biocLite.R")
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biocLite("Biostrings")
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library(Biostrings)
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}
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# Package information:
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# library(help = Biostrings) # basic information
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# browseVignettes("Biostrings") # available vignettes
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# data(package = "Biostrings") # available datasets
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# = 2 Defining the APSES domain ===========================================
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# Load your protein database
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source("makeProteinDB.R")
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# Get the APSES domain sequence for MBP1_MYSPE feature annotation. (You have
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# 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
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(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
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(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
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myDB$annotation$featureID == ftrID])
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(start <- myDB$annotation$start[myDB$annotation$ID == fanID])
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(end <- myDB$annotation$end[myDB$annotation$ID == fanID])
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(apses <- substr(myDB$protein$sequence[myDB$protein$ID == proID],
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start,
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end))
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# The MYSPE "apses" sequence is the sequence that we will use for our reverse
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# 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
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# through its Web API, and to parse results. Have a look at the script, then
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# 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
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# cerevisiae:
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BLASTresults <- BLAST(apses, # MYSPE APSES domain sequence
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db = "refseq_protein", # database to search in
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nHits = 10, #
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E = 0.01, #
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limits = "txid559292[ORGN]") # S. cerevisiae S288c
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length(BLASTresults$hits) # There should be at least one hit there. Ask for advice
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# in case this step fails.
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# = 4 Analysing results ===================================================
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(topHit <- BLASTresults$hits[[1]]) # Get the top hit
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# What is the refseq ID of the top hit
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topHit$accession
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# If this is "NP_010227.1" you have confirmed the RBM of the MYSPE apses
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# domain. If it is not, ask me for advice.
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# [END]
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