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Scoring DNA sequences
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The main objective of this paper is to analyze various DNA sequences to predict the changes that occur in DNA during evolution (mutations). We used a similarity score as a fitness measure to detect symmetry relations, which is appropriate for numerous extremely long sequences.
13p
guernsey
28-12-2021
13
0
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The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome.
11p
vibeauty
23-10-2021
6
1
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New technologies for analyzing biological samples, like next generation sequencing, are producing a growing amount of data together with quality scores. Moreover, software tools (e.g., for mapping sequence reads), calculating transcription factor binding probabilities, estimating epigenetic modification enriched regions or determining single nucleotide polymorphism increase this amount of position-specific DNA-related data even further.
9p
vikentucky2711
26-11-2020
12
1
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Modern DNA sequencing methods produce vast amounts of data that often requires mapping to a reference genome. Most existing programs use the number of mismatches between the read and the genome as a measure of quality.
17p
vikentucky2711
26-11-2020
13
0
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Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between a specific transcription factor and the DNA, these scores are not directly comparable between different transcription factors.
13p
vikentucky2711
24-11-2020
5
1
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Phred quality scores are essential for downstream DNA analysis such as SNP detection and DNA assembly. Thus a valid model to define them is indispensable for any base-calling software. Recently, we developed the base-caller 3Dec for Illumina sequencing platforms, which reduces base-calling errors by 44-69% compared to the existing ones.
14p
viflorida2711
30-10-2020
13
2
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Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used for this purpose.
15p
vijisoo2711
27-10-2020
10
0
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The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching.
5p
caygaocaolon1
13-11-2019
15
0
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