
Sequence alignments
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Bài giảng Tin sinh học đại cương - Chương 3: Bắt cặp trình tự (Sequence Alignment) giới thiệu chung và tập trung làm rõ hiện tượng bắt cặp hai trình tự, bắt cặp nhiều trình tự. Bài giảng hữu ích với các bạn chuyên ngành Sinh học.
37p
maiyeumaiyeu26
23-12-2016
119
24
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In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.[1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
29p
trautuongquan
25-02-2013
43
5
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Chương này gồm có những nội dung chính sau: Giới thiệu tóm tắt về dự án Human Genome; bài toán sequence alignment: Các vấn đề cần giải quyết, scoring system, lập trình động cho vấn đề pairwise alignment; bài toán local sequence alignment. Mời tham khảo.
32p
tangtuy12
02-06-2016
55
4
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The tree sequence based translation model allows the violation of syntactic boundaries in a rule to capture non-syntactic phrases, where a tree sequence is a contiguous sequence of subtrees. This paper goes further to present a translation model based on non-contiguous tree sequence alignment, where a non-contiguous tree sequence is a sequence of sub-trees and gaps. Compared with the contiguous tree sequencebased model, the proposed model can well handle non-contiguous phrases with any large gaps by means of non-contiguous tree sequence alignment. ...
9p
hongphan_1
14-04-2013
34
3
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This paper presents a translation model that is based on tree sequence alignment, where a tree sequence refers to a single sequence of subtrees that covers a phrase. The model leverages on the strengths of both phrase-based and linguistically syntax-based method. It automatically learns aligned tree sequence pairs with mapping probabilities from word-aligned biparsed parallel texts.
9p
hongphan_1
15-04-2013
29
1
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Visualization of multiple sequence alignments often includes colored symbols, usually characters encoding amino acids, according to some (physical) properties, such as hydrophobicity or charge. Typically, color schemes are created manually, so that equal or similar colors are assigned to amino acids that share similar properties.
12p
vicolorado2711
22-10-2020
3
0
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Recently developed methods of protein contact prediction, a crucially important step for protein structure prediction, depend heavily on deep neural networks (DNNs) and multiple sequence alignments (MSAs) of target proteins.
15p
vicolorado2711
23-10-2020
6
0
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Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny.
8p
viconnecticut2711
28-10-2020
7
0
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The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level.
10p
viflorida2711
30-10-2020
4
0
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The alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics. In spite of considerable research and efforts that have been recently deployed for improving the performance of multiple sequence alignment (MSA) algorithms, finding a highly accurate alignment between multiple protein sequences is still a challenging problem.
11p
vioklahoma2711
19-11-2020
2
0
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Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools.
11p
vioklahoma2711
19-11-2020
2
0
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Reconstruction of multiple sequence alignments (MSAs) is a crucial step in most homology-based sequence analyses, which constitute an integral part of computational biology. To improve the accuracy of this crucial step, it is essential to better characterize errors that state-of-the-art aligners typically make.
19p
vioklahoma2711
19-11-2020
1
0
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This paper describes a new MSA tool called PnpProbs, which constructs better multiple sequence alignments by better handling of guide trees. It classifies sequences into two types: normally related and distantly related.
11p
vioklahoma2711
19-11-2020
8
0
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Alternative sequence alignment algorithms yield different results. It is therefore useful to quantify the similarities and differences between alternative alignments of the same sequences. These measurements can identify regions of consensus that are likely to be most informative in downstream analysis.
6p
vioklahoma2711
19-11-2020
2
0
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Alignment of large and diverse sequence sets is a common task in biological investigations, yet there remains considerable room for improvement in alignment quality. Multiple sequence alignment programs tend to reach maximal accuracy when aligning only a few sequences, and then diminish steadily as more sequences are added.
14p
vikentucky2711
24-11-2020
1
0
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A standard procedure in many areas of bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types of analysis. However, downstream results may be highly sensitive to the alignment used, and neglecting the uncertainty in the alignment can lead to significant bias in the resulting inference.
26p
vikentucky2711
24-11-2020
5
0
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Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between residues derived from covariation maps can be sufficient to predict a protein fold.
12p
vikentucky2711
26-11-2020
2
0
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Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment case.
18p
vikentucky2711
26-11-2020
3
0
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In this paper, we consider and improve the global progressing algorithm by using the cache storage technique to make the best of the previous alignment results. This algorithm and cache technique were been developed on the distributed system and Grid computing environment in order to decrease the algorithms execution time, as well as increase the quantity and size of input sequences.
6p
girlsseek
27-02-2019
8
0
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Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evolutionary substitution events derived from a set of aligned sequences.
14p
viflorida2711
30-10-2020
8
0
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