ARSA search protocol

  # Run blast:
  blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -m 8 -b 10000 -i ARSA.fas > ARSA.blast

# find unique matches
cut -f 2 ARSA.blast | uniq > ARSA.blast.matchIDs.uniq
uniq -w 44 ARSA.blast > ARSA.blast.uniq

# use R to plot: 
# within R: histogram of log10 Evalue for blast run
blastTable = read.table("ARSA.blast.uniq")
pdf("ARSA_blastHistogram_eVal.pdf")
logeval.hist <- hist(log10(blastTable$V11), breaks=100, plot=FALSE) 
plot(logeval.hist, col="blue", main="BLAST logarithm of E-values", xlab="lg(E-Value)")
dev.off()

# within R: histogram of %identity for blast run
blastTable = read.table("ARSA.blast.uniq")
pdf("ARSA_blastHistogram_id.pdf")
id.hist <- hist(blastTable$V3, breaks=5, plot=FALSE)
plot(id.hist, col="blue", main="BLAST sequence identity distribution", xlab="percent identity")
dev.off()

 # create lists of Uniprot IDs for analysis for GO annotations
 grep -n "1e-10" ARSA.blast.uniq
 tail -n +1721 ARSA.blast.uniq > ARSA.blast.uniq.worseE10
 cut -f 2 ARSA.blast.uniq.worseE10  > ARSA.blast.uniq.worseE10.matchIDs
 cut -d "|" -f 2 ARSA.blast.uniq.worseE10.matchIDs > ARSA.blast.uniq.worseE10.matchIDs.clean