HW1

1. Learn Perl programming language and learn bioinformatics using it.

a. Install and Learn BioPerl
b. Make a Perl program translating 'all' combinations of triple bases into amino acids
c. Pick 5 protein sequences and predict their secondary structures using available prediction programs
d. Open and re-write one FASTA file containing one protein sequence of TERT
e. Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file
f. Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file
g. In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc
h. Align two protein sequences using a dynamic programming method in Perl
i. Randomly generate five 100 AA long protein sequences and store them in a FASTA file
j. Create a flat text file database of protein sequences with hash function in Perl