Repetitive Dna And Next Generation Sequencing Computational Challenges And Solutions Pdf

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DNA sequencing is the process of determining the nucleic acid sequence — the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine , guanine , cytosine , and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis , biotechnology , forensic biology , virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, [3] characterize antibody repertoire, [4] and can be used to guide patient treatment.

DNA sequencing

Metrics details. Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome. This problem is exacerbated when dealing with repetitive sequences such as transposable elements that occupy half of the mammalian genome mass. Sequenced reads coming from these regions introduce ambiguities in the mapping step. Therefore, applying dedicated parameters and algorithms has to be taken into consideration when transposable elements regulation is investigated with sequencing datasets. Here, we used simulated reads on the mouse and human genomes to define the best parameters for aligning transposable element-derived reads on a reference genome.

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References 1. Pop M. Genome assembly reborn: recent computational challenges , Briefings in Bioinformatics , vol. Treangen and S. DOI :

Repetitive DNA and next-generation sequencing: computational challenges and solutions

Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Treangen and S. Treangen , S. Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs.


Repetitive DNA and next-generation sequencing: Computational challenges and solutions. November ; Nature Reviews Genetics.


Erratum: Repetitive DNA and next-generation sequencing: computational challenges and solutions

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Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results.

Next-generation sequencing NGS technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings. In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks overlap graph-based, de Bruijn graph-based and string graph-based , and introduce the characteristics of each assembly tool and their adaptation scene.

The most valuable application of next generation sequencing NGS technology is genome sequencing. Genomes of several aquatic models had been sequenced in the past few years due to their importance in genomics, development biology, toxicology, pathology, and cancer research.

chapter and author info

В том, что касалось Мидж Милкен, существовали две вещи, которые никому не позволялось ставить под сомнение. Первой из них были предоставляемые ею данные. Бринкерхофф терпеливо ждал, пока она изучала цифры. - Хм-м, - наконец произнесла.  - Вчерашняя статистика безукоризненна: вскрыто двести тридцать семь кодов, средняя стоимость - восемьсот семьдесят четыре доллара.

Хейл взвыл от боли, и все его тело сразу же обмякло. Он скатился набок, сжавшись в клубок, а Сьюзан, высвободившись из-под него, направилась к двери, отлично понимая, что у нее не хватит сил ее открыть. Но тут ее осенило. Она остановилась у края длинного стола кленового дерева, за которым они собирались для совещаний. К счастью, ножки стола были снабжены роликами. Упираясь ногами в толстый ковер, Сьюзан начала изо всех сил толкать стол в направлении стеклянной двери. Ролики хорошо крутились, и стол набирал скорость.

У Бринкерхоффа подогнулись колени. Он не мог понять, почему Мидж всегда права. Он не заметил отражения, мелькнувшего за оконным стеклом рядом с. Крупная фигура возникла в дверях директорского кабинета. - Иису… - Слова застряли у Бринкерхоффа в глотке.  - Ты думаешь, что в ТРАНСТЕКСТ проник вирус. Мидж вздохнула: - А что еще это может .

 - Сейчас найду. Вот.

Я хотел спросить… - Черт тебя дери, Джабба! - воскликнула Мидж.  - Именно это я и пыталась тебе втолковать. - Возможно, ничего страшного, - уклончиво сказал он, - но… - Да хватит .

DNA sequencing

При росте более ста восьмидесяти сантиметров он передвигался по корту куда быстрее университетских коллег. Разгромив очередного партнера, он шел охладиться к фонтанчику с питьевой водой и опускал в него голову.