Nucleotide BLAST: Align two or more sequences using BLAST
Multiple Sequence Alignment and Analysis with Jalview
Need at least 8 sequences Reference: SALIGN - automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter values. Multiple alignments are guided by a dendrogram computed from a matrix of all pairwise alignment scores.
If two multiple sequence alignments of related proteins are input to the server, a profile-profile alignment is performed. AlignMe for Alignment of Membrane Proteins is a very flexible sequence alignment program that allows the use of various different measures of similarity. Khafizov K et al. Gene Context Tool - is an incredible tool for visualizing the genome context of a gene or group of genes synteny.
The degree to which an amino or nucleic acid position is evolutionarily conserved is strongly dependent on its structural and functional importance; rapidly evolving positions are variable while slowly evolving positions are conserved.
The results are presented in colour. This service also provides phylogenetic analysis of the data. The stacked alignments are viewed in Jalview or as sequence logos.
The database search uses the suffix array neighborhood search SANS method, which has been re-implemented as a client-server, improved and parallelized. LocARNA outputs a multiple alignment together with a consensus structure. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.
Alternatively, you can also provide base pair probability matrices dot plots in. If you provide fixed structures, only those structures and not the entire ensemble of possible structures is aligned.
Nucleic Acids Reseach Alternative presentations of alignments: Multiple Align Show - Bioinformatics. Sequence comparison between two small genomes: For additional information on the output see here. This site appears to work best with Internet Explorer. Advanced PipMaker - aligns two DNA sequences and returns a percent identity plot of that alignment, together with a traditional textual form of the alignment.
Produces similar diagrams to the above mentioned programs, but with better control on output. The detailed explanation of this algorithm can be found in . The time and space complexity of this algorithm is 0 mnand if both sequences have approximately the same length, n, we get O n2. To obtain global alignments, the algorithm proposed by  is used. In this algorithm, some minor changes are made to the previously described algorithm.Multiple Sequence Alignment
First, negative values are allowed and, thus, entries are still computed using equation 1 but the fourth condition no longer exists.
Second, the first row and column of array A are filled with the gap penalty, as shown in figure 4. In the case of global alignment, only one alignment is produced for each pair of sequences. Sequential Implementation To obtain local alignments, we implemented a variant of the Smith-Waterman algorithm that uses two linear arrays .
The bidimensional array was not used since, for large sequences, the memory overhead would be prohibitive. The idea behind this algorithm is that it is possible to simulate the filling of the bidimensional array just using two rows in memory, since, to compute entry A[i,j] we just need the values of A[i-1, j], A[i-1, j-1] and A[i,j-1]. So, the space complexity of this version is linear, O n. The time complexity remains O n2.
First, one of the arrays is initialized with zeros.
MAFFT - a multiple sequence alignment program
Then, each entry of the second array is obtained from the first one with the Smith-Waterman algorithm, but using a single character of s on each step. Besides this value, each entry contains: These information allow us to keep a candidate optimal alignment with a score greater than a certain value. When computing the A[i,j] entry, all the information of A[i-1, j], A[i-1, j-1] or A[i,j-1] is passed to the current entry.
To obtain the above values for each entry, we used some heuristics proposed by . The minimal and maximal scores are updated accordingly to the current score. The initial coordinates are updated if the flag is 0 and if the value of the maximal score is greater than or equal to the minimal score plus a parameter indicated by the user, where this parameter indicates a minimum value for opening this alignment as a candidate to an optimal alignment.
If it is the case, the flag is updated to 1, and the initial coordinates change to the current position of the array. The final coordinates are updated if the flag is 1 and if the value of the current score is less than or equal to the maximal score minus a parameter, where the parameter indicates a value for closing an alignment. In this case, this alignment is closed and passed to a queue alignments of the reached optimal alignments and the flag is set to 0.
The gaps, matches and mismatches counters are employed when the current score of the entry being computed comes from more than one previous entry. In this case, they are used to define which alignment will be passed to this entry. In this heuristic , gaps are penalized and matches and mismatches are rewarded. The greater value will be considered as the origin of the current entry. These counters are not reset when the alignments are closed, because the algorithm works with long sequences, and the scores of candidate alignments can begin with good values, turn down to bad values and turn again to good values.
If these values are still the same, our preference will be to the horizontal, to the vertical and at last to the diagonal arrow, in this order.
This is a trial to keep together the gaps along the candidate alignment . At the end of the algorithm, the coordinates of the best alignments are kept on the queue alignments. This queue is sorted by subsequence size and the repeated alignments are removed. To obtain the global alignments, the queue alignments is accessed to obtain the begin and end coordinates of sequences s and t which determine the subsequences where the similarity regions reside.
For each subsequence of s and t obtained this way, the global alignment algorithm proposed by  is executed. Distributed Shared Memory Systems Distributed Shared Memory has received a lot of attention in the last few years since it offers the shared memory programming paradigm in a distributed or parallel environment where no physically shared memory exists.
SVM implements a single paged, virtual address space over a network of computers. It works basically as a virtual memory system. Local references are executed exclusively by hardware. When a non resident page is accessed, a page fault is generated and the SVM system is contacted.
- Multiple alignment program for amino acid or nucleotide sequences
Instead of fetching the page from disk, as do the traditional virtual memory systems, the SVM system fetches the page from a remote node and restarts the instruction that caused the trap. Relaxed memory models aim to reduce the DSM coherence overhead by allowing replicas of the same data to have, for some period of time, different values . By doing this, relaxed models no longer guarantee strong consistency at all times, thus providing a programming model that is complex since, at some instants, the programmer must be conscious of replication.
Hybrid memory models are a class of relaxed memory models that postpone the propagation of shared data modifications until the next synchronization point . These models are quite successful in the sense that they permit a great overlapping of basic memory operations while still providing a reasonable programming model. The goal of Scope Consistency ScC  is to take advantage of the association between synchronization variables and ordinary shared variables they protect.
In Scope Consistency, executions are divided into consistency scopes that are defined on a per lock basis. Only synchronization and data accesses that are related to the same synchronization variable are ordered. The association between shared data and the synchronization variable lock that guards them is implicit and depends on program order.
Additionally, a global synchronization point can be defined by synchronization barriers . Each shared page has a home node.
A page is always present in its home node and it is also copied to remote nodes on an access fault. There is a fixed number of remote pages that can be placed at the memory of a remote node. When this part of memory is full, a replacement algorithm is executed.
The functions that implement lock acquire, lock release and synchronization barrier in JIAJIA are jia lock, jia unlock and jia barrier, respectively . The parallelization strategy that is traditionally used in this kind of problem is known as the "wave-front method" since the calculations that can be done in parallel evolve as waves on diagonals.
Figure 5 illustrates the wave-front method.
Local DNA sequence alignment in a cluster of workstations: algorithms and tools
At the beginning of the computation, only one node can compute value a[1,1]. After that, values a[2,1] and a[1,2] can be computed in parallel, then, a[3,1], a[2,2] and a[1,3] can be computed independently, and so on. The maximum parallelism is attained at the main matrix anti-diagonal and then decreases again. We propose a parallel version of the algorithm presented in section 2. Each processor p acts on two rows, a writing row and a reading row.
Work is assigned in a column basis, i. For the sake of simplicity, we represented in figure 6 the whole similarity array. However, each processor works in fact with two rows, as explained in the previous paragraph. When a processor finishes calculating a row, it copies this row to the reading row and starts calculating the next row, which is now the writing row. Barriers are only used at the beginning and at the end of computation. At the end of the computation of this first phase, the queue alignments contains the best local alignments found by our algorithm.
In the proposed algorithm, the queue alignments is treated as a vector sorted by subsequence size and we use a scattered mapping approach  to assign similarity regions to processors. This strategy eliminates the need of synchronization operations, such as those provided by locks and condition variables.
For each position it accesses, the processor retrieves the begin and end coordinates of the subsequences corresponding to the local alignment. After that, it compares the subsequences using the global alignment algorithm described in section 2. Each processor is responsible for recording the results of the global alignments it performs.
After all global alignments are performed, the processors write their results in a shared vector. In this way, no locks or condition variables are used.
Our results were obtained with real DNA sequences obtained from www. Execution times for each n x n sequence comparisons, where n is the size of both sequences, with 1, 2, 4 and 8 processors are shown in table 1. Figure 7 shows the absolute speedups, which were calculated considering the total execution times and thus include times for initialization and collecting results.
As can be seen in figure 7for small sequence sizes, e. As long as sequence sizes increase, better speedups are obtained since more work can be done in parallel. This effect can be better noticed in figure 8which presents a breakdown of the execution time of each sequence comparison.
For this task, we used two 50K mithocondrial genomes, Allomycesacrogynus and Chaetosphaeridium globosum. In table 2we present a comparison between these programs, showing the coordinates of the alignments with the best scores found by them.
Still in table 2we can note that the results obtained by both programs are very close but they are not the same. This can be explained since both programs use heuristics that involve different parameters.
We also developed a tool to visualize the alignments found by GenomeDSM . An example can be seen in figure 9. We note that the user can make zoom in a particular region and obtain more details of the desired alignment. In phase 2, for each similarity region, global alignments of subsequences are generated. Figure 10 shows the execution times to globally align,and pairs of subsequences obtained from the similarity regions with 1, 2, 4 and 8 processors.
In order to evaluate the results of this second phase, we varied the parameter minimal score, that defines which alignments are considered relevant. Small values for minimal scores generate more similarity regions and, consequently, more pairs to be compared. In figure 9similarity regions are represented. In figure 10this result is labeled as pairs.
The average size of the subsequences is bytes. Figure 10 shows the speedups obtained in this process. An example of the results produced by this second phase is illustrated in figure The distributed algorithm we proposed to globally align subsequences uses a scattered mapping scheme, which is quite effective, since no synchronization is needed to obtain work from the shared queue.
For this reason, we were able to obtain very good speedups, e. Also, the speedup obtained apparently does not depend on the shared queue size. This can be seen in figure Speedups for 2 and 4 processors are between 2 and 1.