Question: 5 FAsta file input and showing result using nested loop
0
gravatar for mubarakkham2016
2.5 years ago by
mubarakkham20160 wrote:

a. Read five different protein sequences from any public repository and store them in five different files in your hard drive.

b. Using nested loop, read each file with following combination and apply global pairwise alignment on sequences. For scoring, use BLOSUM100, BLOSUM62 and BLOSUM45 scoring matrix:

like: file1- file2, file1-3, file1- file4, file1- file5, file2- file3, file2- file4, file2- file5, file3-file4, file3- file5, file4- file5

c. Show histogram of all above scores for each BLOSUM matrix.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by mubarakkham20160
4

Nice questions. Do you need the people here to answer them instead of you? You could get help If you tried something first. Try to answer them and show what you did, then sure people will help you :).

How To Ask Good Questions On Technical And Scientific Forums

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Medhat8.8k
1

This looks a lot like an assignment, and you will learn nothing if someone else solves it for you.

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

It's our past paper. Just trying to solve it for exam prepration

ADD REPLYlink written 2.5 years ago by mubarakkham20160
1

This sounds like someone's homework assignment.

ADD REPLYlink written 2.5 years ago by steve2.6k
library("gdata")
library("csv")
library(seqinr)
library("Biostrings")
library(msa)
library(ape)

choosebank("genbank")
a1 <- read.GenBank("JF806202", as.character = TRUE)
a1
write.fasta(sequences = a1, names = names(a1), nbchar = 80, file.out = "a.fasta")
a2 <- read.GenBank("JF806212", as.character = TRUE)
a2
write.fasta(sequences = a2, names = names(a2), nbchar = 80, file.out = "b.fasta")
a3 <- read.GenBank("JF806213", as.character = TRUE)
a3
write.fasta(sequences = a3, names = names(a3), nbchar = 80, file.out = "c.fasta")
a4 <- read.GenBank("JF806214", as.character = TRUE)
a4
write.fasta(sequences = a4, names = names(a4), nbchar = 80, file.out = "d.fasta")
a5 <- read.GenBank("JF806215", as.character = TRUE)
a5
write.fasta(sequences = a5, names = names(a5), nbchar = 80, file.out = "e.fasta")
a1=read.fasta(file = "a.fasta")
a2=read.fasta(file = "b.fasta")
a3=read.fasta(file = "c.fasta")
a4=read.fasta(file = "d.fasta")
a5=read.fasta(file = "e.fasta")
a1 <- as.character(a1[[1]])
a2 <- as.character(a2[[1]])
a3 <- as.character(a3[[1]])
a4 <- as.character(a4[[1]])
a5 <- as.character(a5[[1]])
q<-c2s(a1)
q1<-c2s(a2)
q2<-c2s(a3)
q3<-c2s(a5)
q4<-c2s(a5)
q<-toupper(q)
q1<-toupper(q1)
q2<-toupper(q2)
q3<-toupper(q3)
q4<-toupper(q4)

r<- matrix(c(q,q, 1, 1), nrow=1)  
r1<- matrix(c(q1,q1, 1, 1), nrow=1)
r2<- matrix(c(q2,q2, 1, 1), nrow=1)
r3<- matrix(c(q3,q3, 1, 1), nrow=1)
r4<- matrix(c(q4,q4, 1, 1), nrow=1)
data("BLOSUM62")
for (a in r) {

   a<-matrix(score(pairwiseAlignment(r, r1,substitutionMatrix = "BLOSUM62")))
}
ADD REPLYlink modified 2.5 years ago by genomax91k • written 2.5 years ago by mubarakkham20160
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