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



Q1. Find all the articles on "cancer" published by Bioinformatics (Oxford, 
England) in 2008.
								[5]

Q2. Find out the ORF for the following sequence:  
>gi|148540055|ref|NM_013748.3| Mus musculus cytokine-dependent hematopoietic cell linker (Clnk), mRNA
CTTACAGAGTGCTCCAGGATGCGACCGTGGACCCCCTTTCCAGGAGCTAGCCGTCTCAACACTGAGCCCT
TGACTAAAGGAAGACTGAGCAGGCTGAGTTGAAGATCCCTCTCCTTTGCCAGGTGCCAAGGACCATGACC
AGCCAGGGCAATAAAAGGACAACGAAAGAAGGATTCGGTGATCTGAGATTCCAGAACGTCTCTCTGCTGA
AAAATAGGTCATGGCCAAGCCTCAGCAGTGCCAAAGGGCGGTGTCGAGCGGTTCTGGAACCACTTCCGGA
TCACAGAAGGAACTTGGCTGGGGTCCCAGGTGGAGAAAAATGCAACAGTAACAACGACTACGAAGATCCT
GAGTTCCAGCTGCTGAAGGCATGGCCATCAATGAAAATTTTACCAGCCAGACCTATCCAGGAATCGGAAT
ACGCAGATACACGCTATTTCCAGGATACGATGGAGGCTCCCCTTCTGTTACCTCCCAAGGCTTCTGTCTC
CACTGAGAGACAAACCAGGGATGTGAGGATGACACATCTGGAAGAAGTGGACAAGCCTACCTTCAAGGAT
GTCAGAAGCCAACGCTTTAAAGGATTCAAATACACAAAAATAAACAAGACTCCTTTGCCACCTCCTCGGC
CTGCTATCACTCTCCCCAAGAAGTACCAACCCTTACCCCCAGCACCACCAGAGGAGAGCAGTGCATACTT
CGCTCCAAAGCCCACCTTTCCAGAAGTCCAGAGGGGGCCCAGGCAGAGGAGTGCAAAAGACTTCAGTAGG
GTCCTTGGAGCAGAAGAAGAATCTCACCACCAGACAAAGCCAGAATCTTCTTGCCCATCATCAAACCAAA
ACACACAGAAGAGTCCACCTGCCATTGCCAGCTCTTCCTACATGCCAGGAAAGCACAGTATACAAGCCAG
AGACCATACAGGTAGCATGCAGCACTGTCCTGCTCAGAGATGCCAAGCTGCAGCCAGCCACAGCCCTCGA
ATGCTGCCCTATGAAAACACAAACTCGGAGAAACCTGACCCCACAAAGCCTGATGAGAAGGATGTCTGGC
AGAATGAATGGTACATTGGAGAATACAGTCGCCAGGCAGTGGAAGATGTGTTAATGAAAGAGAACAAGGA
TGGTACTTTTTTGGTCCGAGACTGCTCTACAAAATCCAAGGCAGAACCATATGTTTTGGTGGTGTTTTAT
GGGAACAAGGTCTACAATGTGAAAATCCGTTTCCTCGAGAGCAATCAACAGTTTGCCCTGGGCACAGGAC
TACGAGGAAATGAGATGTTTGATTCTGTGGAAGACATCATTGAACACTACACATATTTTCCCATTCTGCT
AATAGATGGGAAAGACAAGGCTGCACGCAGGAAACAGTGCTACCTCACCCAGCCACTGCCTCTCGCCAGG
CTCCTTCTCACTCAGTACTCCAGCCAGGCACTTCATGAGTAAGAAGCCCAGCCAGATATCCCCGCATCAG
TGGCCTGGGCCTTGTCTCATTCCTGGCTCAATGGATTCAGTTCTTCTTCCATCTGCATTTATCTCAAAGT
ATTATTTTCTGTGTCTTCAAGGGATGATTTTTTGACTCTGTAAAAA

Report the ORF which you think is the most correct.			[5]

Q3.Search five homologs for antioxidant gene "TPX1" of Arabidopsis thaliana,
and do Multiple sequence alignment.Identify conserve and consesnus region in it.[10]

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



Q5. Search the  Chromosome number, Location, GeneID, MIM, function, other aliases
and Other Designations for gene name "PIK3CA" of Homo sapiens.		[5]

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

>mbt
MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANA
QVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYT
VREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFK
RSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEV
GSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLA
DRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEG
MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLM
AKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASV
EETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV


Q7: Predict the 3D structure of following sequences:			[10]
>biotech
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGR
DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD


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]