Write a perl program that can read a user-specified FASTA file (with just a sing

Question

Write a perl program that can read a user-specified FASTA file (with just a single sequence entry), and tallies and reports

1) the GC-content of the chromosome (i.e. the fraction of bases that are GC),

2) How many bases are 'gaps' (these have N as the 'base'; they indicate un-sequenced regions),

3) How many bases are in non-repetitive regions (these are bases in upper-case), and

4) How many bases are in repetitive regions (these are bases in lower-case).

I have given you a FASTA file to test with, you can use a copy of human chromosome 12, located on elcapitan at /home/biol451sp15/chr12.fa

Note: In this and many FASTA files of entire chromosomes, some bases are in upper-case, and some are in lower-case (the lower-case ones are to indicate repeats.To answer, copy the full file path of your program (located on elcapitan) into the answer box below.For full credit, use strict and use warnings in your program.

Explanation / Answer

1.  The first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since the mammalian radiation, yielding a number of results that would have been difficult to obtain using the more conventional comparative method of analysis. This analysis revealed substantial and consistent variability of rates of substitution, with the variability ranging up to 2-fold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the reverse rates suggesting that much of that variation is due to differences in mutation rates rather than in the probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all types of substitution we observe substantially more hotspots than coldspots, with hotspots showing substantial clustering over tens of Mbp

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