building a multiple sequence alignment

... EGEWQLVLHVWAKV AAEKTKIRSAWAPV ESQAALVKSSWEEF PKVKAHGKKVLGAFSDG L PKVKAHGKKVLHSFGEGV AQVKGHGKKVADALTNAV AQVKAHGKKVGHALTLAV EDLKKHGVTVLTALGAIL ADVRWHAERIINAVNDAV PELQAHAGKVFKLVYEAA LGNVLVCVLAHH LGNVLVVVLARH ... LSHCLLVTLAAH LSHCLLSTLAVH ISRAIIHVLHSR LAAVIADTVAAG VKEAILKTIKEV FGKEFTPPVQA FGKDFTPELQA LPAEFTPAVHA LPNDFTPAVHA HPGDFGADAQG -DA VGAKWSEELNS N-N-GAH GGH EAD YST NAN S7 0.442 VDVEGGEALGRLLVV ... 1.2 and 1.3 give examples of global and local alignments CHAPTER INTRODUCTION HEAGAWGHE-E P-AW-HEAE Figure 1.2: A sample of global sequence alignment AWGHE AW-HE Figure 1.3: A sample of a local...

Ngày tải lên: 26/09/2015, 09:48

... 5’-GGTCTTTAGCAACCCTGA-3’ 18 50 54.6 5’-ATCATCAAGGATTCCAGA-3’ 18 39 48.7 5’-GATCTTTGCTAACCCTGA-3’ 18 44 51.3 5’-CTTTCAAGGGTTCCAGAG-3’ 18 50 53.6 GS1.3 5’-AATCTTCGATCATCCCAA-3’ 5’-AAAGTCTAAAGCTTAGAG-3’ 18 18 39 33 ... 5’-GATCTTCAGCCACCCCGA-3’ 18 61 59.4 739 5’-AATGTGTCATCAACCGAG-3’ 18 44 51.5 5’-GATCTTTGAAGACCCTAG-3’ 18 44 48.8 5’-TCTTTCATGGTTTCCAAA-3’ 18 33 50.1 5’-AGTGCGCATTAAGGACCCATCA-3’ 22 50 61 5’-ACACACTGGCTTCCACAATAGG-3’ ... GS1 Plant Arabidopsis thaliana GS1 Plant Arabidopsis thaliana AtGS1 isoform AF419608 tity AtGS1 isoform AY091101 GS1 Plant GS1 GS1 Plant Plant Arabidopsis thaliana AtGS1 isoform AY088312 Arabidopsis...

Ngày tải lên: 20/12/2015, 08:16

... span iteratively from small one to large one (lines 1-2) This strategy can guarantee that when translating the current span, all spans smaller than the current one have already been translated ... 961-968 Daniel Gildea 2003 Loosely Tree-Based Alignment for Machine Translation ACL-03 80-87 Jonathan Graehl and Kevin Knight 2004 Training tree transducers HLT-NAACL-2004 105-112 Mary Hearne and Andy ... translation HLT-NAACL-03 127133 Philipp Koehn 2004 Pharaoh: a beam search decoder for phrase-based statistical machine translation models AMTA-04, 115-124 Philipp Koehn, Hieu Hoang, Alexandra Birch,...

Ngày tải lên: 17/03/2014, 02:20

... clusters As explained above, tandem duplications pose a hard problem for automatic alignment algorithms Clusters of such paralogous genes are therefore particularly hard to align As a real-life example ... define a universal objective function constitutes a fundamental limitation for all automated alignment algorithms Often a user is already familiar with a sequence family that he or she wants to align, ... our alignment approach Alignment of tandem duplications There are many situations where automated alignment procedures can produce biologically incorrect aligments An obvious challenge are distantly...

Ngày tải lên: 12/08/2014, 17:20

... use a subroutine PAIRWISE _ALIGNMENT (si, sj, A) that takes two sequences si and sj and (optionally) an existing consistent set of fragments A as input and calculates an optimal alignment of si and ... method Next, a subroutine GREEDY _ALIGNMENT (A, F') takes an alignment A and a set of fragments F' as arguments and returns a new alignment A' ⊃ A by adding fragments from Note that it is not ... the sequences are aligned that share some statistically significant similarity, unrelated parts of the sequences remain unaligned This way, the method can produce global as well as local alignments...

Ngày tải lên: 12/08/2014, 17:20

... Metalia spatagus Plagiobrissus grandis Allobrissus agassizii Metalia spatagus Lovenia cordiformis Lovenia cordiformis Echinocardia laevigaster Echinocardia laevigaster Paramaretia multituerculata ... systems are circular (actually, every planar drawing of an X-tree provides such a circular ordering), and that circular split systems are weakly compatible – i.e., A1 ∩ A2 ∩ A3 , A1 ∩ A ∩ A , A1 ∩ A2 ... taxa A split S = A| A = A |A is a bipartition of the set X of taxa, i.e., a partition of X into two disjoint, non-empty subsets A and A Two such splits A1 | A1 and A2 | A of X are called compatible...

Ngày tải lên: 12/08/2014, 17:20

... Sahinalp SC, Zhang K: RNA-RNA interaction prediction and antisense RNA target search Journal of Computational Biology 2006, 13(2):267-82 19 Chitsaz H, Salari R, Sahinalp SC, Backofen R: A partition ... intra-molecular base pairs Square brackets indicate base pairs of the partial structure σp Shown are all columns with < 75% gaps Jalview [33] was used for alignment visualisation and the number of iterations ... multiple alignments of RNA sequences Its rationale is based on the assumption that a non-negligible amount of the RNA-RNA interactions contain compensatory base changes across the binding sites The algorithm...

Ngày tải lên: 12/08/2014, 17:20

... The decoder translates each span iteratively in a bottom up manner which guarantees that when translating a source span, any of its sub-spans is already translated For each source span [j1, j2], ... Machine Translation ACL-03 80-87 Min Zhang, Hongfei Jiang, AiTi Aw, Haizhou Li, Chew Lim Tan and Sheng Li 200 8a A tree sequence alignment- based tree-to-tree translation model ACL08 559-567 Mary ... Equivalence ACL-06 977-984 Jason Eisner 2003 Learning non-isomorphic tree mappings for machine translation ACL-03 Kenji Yamada and Kevin Knight 2001 A syntax-based statistical translation model ACL-01...

Ngày tải lên: 17/03/2014, 01:20

... initialize pheromone trail matrix and m ants; while (stop conditions not satisfied) for each a ∈ A Ant a build a multiple graph alignment; Local search// run only at the second stage Search by changing ... graph as ACO-MGA algorithm does but with more efficient heuristic information and local search procedures General framework of ACO-MGA2 is as follows A General framework After initializing parameters ... vertices Random walk procedure to construct an alignment In each iteration, each ant will repeat the process to build vectors a = (a1 ,…, an) for an alignment A as follows The ant randomly chooses an...

Ngày tải lên: 14/10/2015, 15:23

... entity classes, business rules, and middle-tier caching of data to reduce database roundtrips Data access layer Encapsulates database access and provides an interface that is database and data source ... internal subsystems, which deal with users, pages, widgets, etc The façade is named DashboardFacade (see Figure 2-2) Web layer Business layer Data access layer Default.aspx Dashboard Facade Database ... Database Context Figure 2-2 Default.aspx calls DashboardFacade in the business layer for all operations, which, in turn, uses workflows that work with databases via DatabaseHelper and DatabaseContext...

Ngày tải lên: 15/11/2012, 14:24

... the appropriate electric field value The ray list contains all of the data about rays propagating from a base station to a field point Each field point has a ray list associated with it A ray ... travelling along localized ray paths (i.e approximately a straight line) Therefore, ray tracing can be used as a method for the simulation and approximation of radio wave propagation The ray ... this reason ray tracing can be used as a method for the simulation and approximation of radio wave propagation at high frequencies The ray tracing of radio waves operates in the same manner as optical...

Ngày tải lên: 20/11/2012, 11:36

... 10:47 AM Page 226 CHAPTER 10 ■ BUILDING A SAMPLE APPLICATION USING ASP.NET AJAX Figure 10-1 An ASP NET AJAX-based stock application Understanding the Application Architecture The application ... OnActiveTabChanged="TabContainer1_ActiveTabChanged"> Basic Quote

Ngày tải lên: 05/10/2013, 10:20

... company—for example, a labor strike in a plant that was not expected or anticipated that catches management unprepared A contingency plan should address such occurrences Natural disasters are a ... operational plan sets the strategic plan into motion on a practical level Building a Business Plan in Five Pages 31 The Organizational Plan—Defining Your Corporate Structure The organizational ... will ask, “Has my management had this training? If not, see me after they have participated.” Leadership and Managership Training What I found worked well at a Midwest business-to-business catalogue...

Ngày tải lên: 24/10/2013, 09:20

... or inclination, or a fixed state of mind So, a wealth and prosperity mindset would mean an attitude or inclination that causes us to focus on abundance It may surprise you to learn that most people ... overly-defensive can actually provoke attacks, and being overly-pessimistic can attract more and more issues that prevent us from improving our lives Rather than living with a reactive mindset, you can learn ... wealth are tucked away in a surprising place: in your greatest interests and passions Of course, simply following your passions isn’t enough You also have to find a way to make your passions pay...

Ngày tải lên: 24/10/2013, 16:15

... are directly connected The default Gateway is only required on local area networks that are connected to a router Computer IP Address Subnet mask Default Gateway PC – A 192.168.1.1 255.255.255.0 ... the two PCs a Set the IP address information for each PC according to the information in the table b Note that the default gateway IP address is not required, since these computers are directly ... they can be restored at the end of the lab These include IP address, subnet mask, default gateway, and DNS servers If the workstation is a DHCP client, it is not necessary to record this information...

Ngày tải lên: 27/10/2013, 07:15

... are directly connected The default gateway is only required on local area networks that are connected to a router Computer IP Address Subnet mask Default Gateway PC – A 192.168.1.1 255.255.255.0 ... the two PCs a Set the IP address information for each PC according to the information in the table b Note that the default gateway IP address is not required, since these computers are directly ... they can be restored at the end of the lab These include IP address, subnet mask, default gateway, and DNS servers If the workstation is a DHCP client, it is not necessary to record this information...

Ngày tải lên: 27/10/2013, 07:15

... PCs and the hub will be accomplished using a Category or 5e straight-through patch cable Locate two cables that are long enough to reach from each PC to the hub Attach one end to the NIC and ... these computers are directly connected The default gateway is only required on local area networks that are connected to a router Computer IP Address Subnet mask Default Gateway PC – A 192.168.1.1 ... the example below: Step Configure TCP/IP settings for the two PCs a Set the IP address information for each PC according to the information in the table b Note that the default gateway IP address...

Ngày tải lên: 04/11/2013, 16:15

... patch cable Locate two cables that are long enough to reach from each PC to the switch Attach one end to the NIC and the other end to a port on the switch Be sure to examine the cable ends carefully ... are directly connected The default gateway is only required on local area networks that are connected to a router Computer IP Address Subnet mask Default Gateway PC – A 192.168.1.1 255.255.255.0 ... the two PCs a Set the IP address information for each PC according to the information in the table b Note that the default gateway IP address is not required, since these computers are directly...

Ngày tải lên: 05/11/2013, 12:15