Amity Institute of Biotechnology
Amity University
M.Sc Biotechnology IV sem
Sub: Computational Biology



Q1. Find articles written by the following authors:
a.A K Jitendra
b.S G Hong 
c.M Z Zhang 
d.D A Swanson 								[5]

Q2. Find out the ORF for the following sequence:  NM_013748.
 Report the ORF which you think is the most correct.			[5]

Q3.Search five homologs for MHP2 gene of Homo sapiens,and do Multiple sequence 
alignment.Identify conserve and consesnus region in it.			[10]

Q4. Search motif in following sequences and predict it's funtion.	[10]
>Biotechnology [Homo sapiens]
MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANA
QVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYT
VREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFK
RSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEV
GSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLA
DRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG
MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLM
AKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASV
EETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV



Q5. Search Chromosome number, Location, GeneID, and Other Designation for gene name
"cg" of Drosophila melanogaster.					[5]

Q6: Predict the secondary structure of following sequences:		[5]

>gi|205829174|sp|P04637.3|P53_HUMAN RecName: Full=Cellular tumor antigen p53; 
AltName: Full=Tumor suppressor p53; AltName: Full=Phosphoprotein p53; AltName: 
Full=Antigen NY-CO-13
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGR
DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD


Q7: Predict the 3D structure of following sequences:			[10]
>mbt
MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANA
QVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYT
VREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFK
RSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEV
GSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLA
DRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG
MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLM
AKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASV
EETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV

Q8:Report the models, energy of the models, Ramachandran plot, Superimposed images 
of the model and the RMSD values for the above predicted structure.	[10]


Q9: Viva								[20]

Q10: File								[20]