Read FASTA into a dataframe and extract subsequences of FASTA file
I have a small fasta file of DNA sequences which looks like this:
>NM_000016 700 200 234
ACATATTGGAGGCCGAAACAATGAGGCGTGATCAACTCAGTATATCAC
>NM_000775 700 124 236
CTAACCTCTCCCAGTGTGGAACCTCTATCTCATGAGAAAGCTGGGATGAG
>NM_003820 700 111 222
ATTTCCTCCTGCTGCCCGGGAGGTAACACCCTGGACCCCTGGAGTCTGCA
Questions:
1) How can I read this fasta file into R as a dataframe where each row is a sequence record, the 1st column is the refseqID and the 2nd column is the sequence.
2) How to extract subsequence at (start, end) location?
NM_000016 1 3 #"ACA"
NM_000775 2 6 #"TAACC"
NM_003820 3 5 #"TTC"
Answer
You should have a look at the Biostrings package.
library("Biostrings")
s = readDNAStringSet("nm.fasta")
subseq(s, start=c(1, 2, 3), end=c(3, 6, 5))