...Name: CHEN LIN Student ID: 44141569-3 11300A Bioinformatics Homework 2 Nov. 18, 2014 1. Sequence Alignment Using Dynamic Programming (DP) There are two amino acid sequences, seq1: COELACANTH and seq2: PELICAN. Obtain the global alignment by using DP (the Needleman-Wunsch algorithm) . $+ 1 for letter that match ! Scoring scheme : #- 1 for mismatches !- 1 for gaps " Answer: ————————————————————————— C O E L A C A N T H P E L I C A N ————————————————————————— -1 -1 1 1 -1 1 1 1 -1 -1 λ λ P E L I C A N Seq1 Seq2 C -1 -1 -2 -3 -4 -3 -4 -5 O P O -2 -2 -2 -3 -4 -4 -4 -5 E E E -3 -3 -1 -2 -3 -4 -5 -5 L L L -4 -4 -2 0 -1 -2 -3 -4 A I A -5 -5 -3 -1 -1 -2 -1 -2 C C C -6 -6 -4 -2 -2 0 -1 -2 A A A -7 -7 -5 -3 -3 -1 1 0 N -8 -8 -6 -4 -4 -2 0 2 N N T -9 -9 -7 -5 -5 -3 -1 1 T — H -10 -10 -8 -6 -6 -4 -2 0 H — 0 -1 -2 -3 -4 -5 -6 -7 C — Name: CHEN LIN Student ID: 44141569-3 Seq1 Seq2 C P O — E E L L A I C C A A N N T — H — 2. In this question you will use two different dot matrix analysis servers to analyze the sequence of the human low density lipoprotein receptor (NP_000518). You will run a dot matrix analysis of this protein against itself (which means you will need to enter its sequence in both boxes on the website). A. First use Dottup (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::dottup). Set the word size to 2 (“word size” is basically the same as “window”). Using a word size of 2, the algorithm will scan a window of 2 amino...
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...INDEX 1.To retrieve the protein or DNA sequence in FASTA format from the NCBI database and analyze the obtained data. 2.For a given protein sequences find the function ,structural relevance and annotation studies by using Uniprot/Uniprot KB. 3.For a given protein, find the protein PDB code ,release date , resolution ,Classification and pub med citation from PDB Structure data base. 4.Find the disease pathway ,drug target enzymes and drug molecules used for a given disease by using KEGG database. 5.For a given protein/enzyme find its EC number ,its location and Km, K cat/Km values by using BRENDA/KEGG database. 6.Find the pair wise sequence alignment for a given protein/DNA sequence by using Dot matrix method Dot helix and comment on the results inverted repeats ,palindromes. 7.For a given Protein sequence find the homolog sequences and Study the obtained output critical statistical parameters, the % identity, %similarity ,p ,E-value by using BLAST. 8.For a given Protein/DNA sequence find the pblast ,nblast ,psi blast ,phi blast ,blast, tbalstn and analyze the obtained results obtained results for each blast method. 9.For a given Protein sequence find the pair wise sequence alignment by using the FASTA algorithm and compare the results obtained with those from other methods. 10.Find the optimal alignment for the given protein sequence by using Dynamic programming –LALIGN method. 11.For a given FASTA sequence find the multiple sequence alignment by using the Clustal...
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...D38–D51 Nucleic Acids Research, 2011, Vol. 39, Database issue doi:10.1093/nar/gkq1172 Published online 20 November 2010 Database resources of the National Center for Biotechnology Information Eric W. Sayers1,*, Tanya Barrett1, Dennis A. Benson1, Evan Bolton1, Stephen H. Bryant1, Kathi Canese1, Vyacheslav Chetvernin1, Deanna M. Church1, Michael DiCuccio1, Scott Federhen1, Michael Feolo1, Ian M. Fingerman1, Lewis Y. Geer1, Wolfgang Helmberg2, Yuri Kapustin1, David Landsman1, David J. Lipman1, Zhiyong Lu1, Thomas L. Madden1, Tom Madej1, Donna R. Maglott1, Aron Marchler-Bauer1, Vadim Miller1, Ilene Mizrachi1, James Ostell1, Anna Panchenko1, Lon Phan1, Kim D. Pruitt1, Gregory D. Schuler1, Edwin Sequeira1, Stephen T. Sherry1, Martin Shumway1, Karl Sirotkin1, Douglas Slotta1, Alexandre Souvorov1, Grigory Starchenko1, Tatiana A. Tatusova1, Lukas Wagner1, Yanli Wang1, W. John Wilbur1, Eugene Yaschenko1 and Jian Ye1 1 Downloaded from http://nar.oxfordjournals.org/ by guest on March 20, 2015 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA and 2University Clinic of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Auenbruggerplatz 3, A-8036 Graz, Austria Received September 16, 2010; Revised October 29, 2010; Accepted November 1, 2010 ABSTRACT In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology...
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...in Bioinformatics for Genomics and Drug Design Bioinformatics is essential to give meaning to the huge mass of biological data that is being produced in the post-genomic era, playing a prominent role in the biomedical and biotechnological research of this century. Bioinformaticians are highly qualified and demanded professionals. They enjoy many positions available on leading research fields as genomics, personalized medicine, drug discovery, biotechnology, crop improvement and other health science research fields. Program strengths The Master of Science in Bioinformatics for Genomics and Drug Design is a novel learning experience that differs from conventional programs in several ways: • Intensive one-year master’s program (60 ECTS). • International degree program. All classes are taught in English. • Highly practical orientation. The MSc in Bioinformatics provides training to create bioinformatics professionals ready to succeed. • Focus on three expertise areas. Genomics, Drug Discovery and High Performance Computing. • Highly qualified faculty. Faculty are leaders of international research groups and prestigious professionals from bioinformatics industry. • Student mentoring programs. • Bioinformatics resources. • Networking and job vacancies. Open positions offered by research groups and companies. • Financial aid may be provided. MSc in Bioinformatics for Genomics and Drug Design Program content and structure Module 1 Programming in Bioinformatics (6 ECTS)...
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...1-16 Protein Motifs Protein motifs may be defined by their primary sequence or by the arrangement of secondary structure elements The term motif is used in two different ways in structural biology. The first refers to a particular amino-acid sequence that is characteristic of a specific biochemical function. An example is the so-called zinc finger motif, CXX(XX)CXXXXXXXXXXXXHXXXH, which is found in a widely varying family of DNA-binding proteins (Figure 1-49). The conserved cysteine and histidine residues in this sequence motif form ligands to a zinc ion whose coordination is essential to stabilize the tertiary structure. Conservation is sometimes of a class of residues rather than a specific residue: for example, in the 12-residue loop between the zinc ligands, one position is preferentially hydrophobic, specifically leucine or phenylalanine. Sequence motifs can often be recognized by simple inspection of the amino-acid sequence of a protein, and when detected provide strong evidence for biochemical function. The protease from the human immunodeficiency virus was first identified as an aspartyl protease because a characteristic sequence motif for such proteases was recognized in its primary structure. The second, equally common, use of the term motif refers to a set of contiguous secondary structure elements that either have a particular functional significance or define a portion of an independently folded domain. Along with the functional sequence motifs, the former are...
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...Homology modeling .Discuss (25) The advent of high throughput technologies such as next generation sequencing has led to generation of a lot of biological data which include protein sequences data. The full understanding of the biological roles of protein requires the knowledge of their structures. Experimental protein structure prediction methods consisting of x-ray crystallography and NMR spectroscopy are time consuming leaving a gap between generation of sequences and structure prediction. Computational approaches can be used to develop protein structure models which can be used for rational design of biochemical experiments which include site directed mutagenesis, protein stability and functional analysis of proteins. There are three computational approaches to three dimensional structure prediction namely homology modeling, threading and ab initio prediction (Xong, 2006). Homology modeling (comparative modeling) is a computational protein structure modeling technique used to build three dimensional (3D) models of proteins of unknown structure ( the target) on the basis of a sequence similarity to proteins of known structure (the template). Two conditions must be met to build a useful model, the similarity between the target sequence and template must be detectable and a substantially correct alignment between the target and the template should be calculated. Homology modelling is possible because small changes in protein sequence result in small changes in its 3D structures...
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...CURRICULUM VITAE NAME: BERNARD NDINI MWENDWA PHONE NUMBER: 0789921182/ 0707343489/0727609248 E-MAIL: benardmwendwa.bm@gmail.com/benardndini@yahoo.com ADDRESS: 16-90214 DOB: 11/7/1992 GENDER: MALE NATIONALITY: KENYAN ID NUMBER: 29808279 RELIGION: CHRISTIAN MARITAL STATUS: SINGLE LANGUAGES: ENGLISH, KISWAHILI (both spoken and written) SUMMARY A hard-working and motivated BSC Biochemistry and Molecular Biology graduate with proven communication, organization and numeracy skills seeking to gain relevant experience to diversify and excel in varying fields. Looking to apply solid knowledge of biochemistry and molecular biology practices to setting and building on skills developed during course work studies. Eager to share the knowledge I have gained. Pro-active and keen to learn, ready to back up the knowledge I have gained with relevant experience .Wishing to make a positive contribution to production and research institutions. EDUCATION BACKGROUND 2012-2015: BSC BIOCHEMISTRY (MOLECULAR BIOLOGY) JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND TECHNOLOGY, SECOND CLASS HONOURS (UPPER DIVISION) Jan 2007 –Nov 2010: KENYA CERTIFICATE OF SECONDARY EDUCATION St JOSEPH’S MUTITO BOYS SECONDARY SCHOOL GRADE ATTAINED:...
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