Question $1.$ Write a program to implement Chou and Fasman method of secondary structure

prediction $($Helix and Beta strand$)$ for the following protein sequence.

Use the following notation $-H$ for Helix, $S$ for Beta strand.

MNASSEGESFAGSVQIPGGTTVLVELTPDIHICGICKQQFNNLDAFVAHKQSGCQLTGTSAAAP

STVQFVSEETVPATQTQTTTRTITSETQTITVSAPEFVFEHGYQTYLPTESNENQTATVISLPA

KSRTKKPTTPPAQKRLNCCYPGCQFKTAYGMKDMERHLKIHTGDKPHKCEVCGKCFSRKDKLKT

HMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDERPFKCQICPYASRNSSQLTVHLRSHTAS

ELDDDVPKANCLSTESTDTPKAPVITLPSEAREQMATLGERTFNCCYPGCHFKTVHGMKDLDRH

LRIHTGDKPHKCEFCDKCFSRKDNLTMHMRCHTSVKPHKCHLCDYAAVDSSSLKKHLRIHSDER

PYKCQLCPYASRNSSQLTVHLRSHTGDTPFQCWLCSAKFKISSDLKRHMIVHSGEKPFKCEFCD

VRCTMKANLKSHIRIKHTFKCLHCAFQGRDRADLLEHSRLHQADHPEKCPECSYSCSSAAALRV

HSRVHCKDRPFKCDFCSFDTKRPSSLAKHVDKVHRDEAKTENRAPLGKEGLREGSSQHVAKIVT

QRAFRCETCGASFVRDDSLRCHKKQHSDQSENKNSDLVTFPPESGASGQLSTLVSVGQLEAPLE

PSQDL

a$)$ Display the sequence regions that are helical in nature.

$(20$ marks$)$

b$)$ Display the sequence regions that have the tendency to form beta strands.

$(20$ marks$)$

c$)$ Display the conflicting regions. Also solve these conflicts to reach to the final assignment of

secondary structural elements. Display the output for the complete sequence.

$(10$ marks$)$

Use the Chou and Fasman parameters provided on the next page for all the calculations in your

program.

Chou and Fasman parameters to be used for the prediction are as following: