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Sensitive alignment
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In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate.
11p
vioraclene
31-03-2024
4
2
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Clinical prediction models providing binary categorizations for clinical decision support require the selection of a probability threshold, or “cutpoint,” to classify individuals. Existing cutpoint selection approaches typically optimize test-specific metrics, including sensitivity and specificity, but overlook the consequences of correct or incorrect classification.
11p
vighostrider
25-05-2023
3
2
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We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps.
17p
vielonmusk
30-01-2022
5
0
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RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads.
13p
vielonmusk
30-01-2022
9
0
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Varlociraptor: Enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of uncertainties related to gap and alignment ambiguities, twilight zone indels, cancer heterogeneity, sample purity, sampling, and strand bias.
25p
viarchimedes
26-01-2022
8
0
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The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded by the rapid growth of sequence databases.
10p
viwyoming2711
16-12-2020
17
0
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The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result.
8p
vikentucky2711
26-11-2020
10
0
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The Smith-Waterman algorithm is known to be a more sensitive approach than heuristic algorithms for local sequence alignment algorithms. Despite its sensitivity, a greater time complexity associated with the Smith-Waterman algorithm prevents its application to the all-pairs comparisons of base sequences, which aids in the construction of accurate phylogenetic trees.
15p
vikentucky2711
24-11-2020
6
1
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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
13
1
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Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods.
8p
vioklahoma2711
19-11-2020
8
0
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Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species.
13p
viconnecticut2711
29-10-2020
4
1
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Alignment of sequence families described by profiles provides a sensitive means for establishing homology between proteins and is important in protein evolutionary, structural, and functional studies.
13p
vijisoo2711
27-10-2020
9
1
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Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data.
9p
vicolorado2711
23-10-2020
8
0
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Banana bract mosaic disease (BBrMD) is one of the most important viral diseases of banana which leads to a yield reduction. We have identified banana bract mosaic virus (BBrMV) in banana plants growing in the regions of southern India based on symptomatology, sequence homology, and Serodiagnostic assays. The viral sequence encoding the coat protein was specifically amplified by RT-PCR (Reverse Transcriptase – Polymerase chain reaction) using specific primers bordering the Coat Protein (CP) gene.
12p
cothumenhmong1
10-12-2019
16
0
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Physiological parameters and expression levels of drought related genes were analyzed in early vegetative stage of two bread wheat cultivars (Sids and Gmiza) differ in drought tolerance capacity. Both cultivars were imposed to gradual water depletion started on day 17 till day 32 after sowing. Sids, the more tolerant cultivar to drought showed higher fresh and dry weights than the drought sensitive genotype, Gmiza.
10p
trinhthamhodang1
16-11-2019
13
1
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We use a machine learner trained on a combination of acoustic and contextual features to predict the accuracy of incoming n-best automatic speech recognition (ASR) hypotheses to a spoken dialogue system (SDS). Our novel approach is to use a simple statistical User Simulation (US) for this task, which measures the likelihood that the user would say each hypothesis in the current context. Such US models are now common in machine learning approaches to SDS, are trained on real dialogue data, and are related to theories of “alignment” in psycholinguistics.
9p
bunthai_1
06-05-2013
47
1
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Aligning sentences belonging to comparable monolingual corpora has been suggested as a first step towards training text rewriting algorithms, for tasks such as summarization or paraphrasing. We present here a new monolingual sentence alignment algorithm, combining a sentence-based TF*IDF score, turned into a probability distribution using logistic regression, with a global alignment dynamic programming algorithm. Our approach provides a simpler and more robust solution achieving a substantial improvement in accuracy over existing systems. ...
8p
bunthai_1
06-05-2013
53
1
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Mapping documents into an interlingual representation can help bridge the language barrier of a cross-lingual corpus. Previous approaches use aligned documents as training data to learn an interlingual representation, making them sensitive to the domain of the training data. In this paper, we learn an interlingual representation in an unsupervised manner using only a bilingual dictionary.
6p
hongdo_1
12-04-2013
45
4
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We introduce a discriminatively trained, globally normalized, log-linear variant of the lexical translation models proposed by Brown et al. (1993). In our model, arbitrary, nonindependent features may be freely incorporated, thereby overcoming the inherent limitation of generative models, which require that features be sensitive to the conditional independencies of the generative process.
11p
hongdo_1
12-04-2013
33
2
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Second, explicitly analyzing fees allows us to determine whether investors in SRI funds pay an explicit price for the ethical value of their investments. Our results also shed light on the way in which mutual fund fees are determined, particularly on the question of whether fees simply reflect funds' operating costs or, as argued by Christofersen and Musto (2002) and Gil-Bazo and Ruiz-Verdú (2009), they are set taking into account the performance sensitivity of funds' clienteles.
286p
khanhchilam
29-03-2013
53
11
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