scholarly journals Compression of DNA sequence reads in FASTQ format

2011 ◽  
Vol 27 (6) ◽  
pp. 860-862 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Szymon Grabowski
Keyword(s):  
Dna Sequence ◽  
Fastq Format

scholarly journals Fastq-pair: efficient synchronization of paired-end fastq files

2019 ◽  
Author(s):  
John A. Edwards ◽  
Robert A. Edwards
Keyword(s):  
Dna Sequence ◽  
Efficient Solution ◽  
Bioinformatics Analysis ◽  
Sequence Data ◽  
Additional Information ◽  
Fastq Format ◽  
Separate File ◽  
The One ◽  
Computational Resources ◽  
Memory Efficient

AbstractPaired end DNA sequencing provides additional information about the sequence data that is used in sequence assembly, mapping, and other downstream bioinformatics analysis. Paired end reads are usually provided as two fastq-format files, with each file representing one end of the read. Many commonly used downstream tools require that the sequence reads appear in each file in the same order, and reads that do not have a pair in the corresponding file are placed in a separate file of singletons. Although most sequencing instruments capable of generating paired end reads produce files where each read has a corresponding mate, many downstream bioinformatics manipulations break the one-to-one correspondence between reads, and paired-end sequence files loose synchronicity, and contain either unordered sequences or sequences in one or other file without a mate. Trivial solutions to this problem require reading one or both of the DNA sequence files into memory but quickly become limited by computational resources for moderate to large sized sequence files that are common nowadays. Here, we introduce a fast and memory efficient solution, written in C for portability, that synchronizes paired-end fastq files for subsequent analysis and places unmatched reads into singleton files.Fastq-pair is freely available from https://github.com/linsalrob/fastq-pair and is released under the MIT license.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Phylogenetic relationships ofSalvia(Lamiaceae) in China: Evidence from DNA sequence datasets

2012 ◽  
pp. n/a-n/a
Author(s):  
Qian-Quan Li ◽  
Min-Hui Li ◽  
Qing-Jun Yuan ◽  
Zhan-Hu Cui ◽  
Lu-Qi Huang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships

Corrected DNA Sequence of the Platelet Glycoprotein IX Gene

1997 ◽  
Vol 77 (05) ◽  
pp. 1034-1035 ◽  
Author(s):  
Tomohiro Hayashi ◽  
Keijiroh Suzuki ◽  
Akito Yahagi ◽  
Jiroh Akiba ◽  
Katsushi Tajima ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Platelet Glycoprotein

The Conceptualist Ends of Writing and the End of Conceptualism

CounterText ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 63-77
Author(s):  
Louis Armand
Keyword(s):  
Dna Sequence ◽  
Life Form ◽  
The Sun

This essay examines the convergence of conceptualist poetics with evolutionary code as a form of ‘becoming alien’. The focus is Christian Bök's The Xenotext project: an attempt at translating a ‘short verse about language and genetics’, using a chemical alphabet, into a DNA sequence implanted into the genome of a polyextremophile bacterium capable of enduring conditions in outerspace. Bök describes the project as, ‘in effect, engineering a life-form so that it becomes not only a durable archive for storing a poem, but also as an operant machine for writing a poem – one that can persist on the planet until the sun itself explodes …’. The concrete, constraint-based character of Bök's project evokes a mode of writing between posthumanist aesthetics and a positivist grammatology by turns deconstructive and itself requiring of deconstruction.

Sign in / Sign up

Export Citation Format

Share Document