Sentences with phrase «read sequencing with»

Dr. Brian Bodemann, Account Manager, West «Advancing QC for long read sequencing with the FEMTO Pulse»

Not exact matches

With all due respect, if you'd read the actual study, you would see that this was not a whole genome sequence comparison; rather it was a comparison of mitochondrial 12S rDNA and 16S rDNA sequences for the purposes of confirming the species relationship between the Pod Mrcaru lizards (P. sicula), the source population from Pod Kopiste (also P. sicula), and the original indigenous population on Pod Mrcaru (P. mellisellensis).

Stool samples were dominated by Bacteroides and Bifidobacterium comprising half of sequence reads, with Streptococcus, Clostridium, Enterococcus, Blautia, Veillonella, Lactobacillus, Staphylococcus, Planococcus, and others representing the remainder (Table 2).

Now that all three volumes of Mullin's diaries are published, it's advisable to read them in sequence — they will provide historians with as much of a valuable insight into New Labour as into the diarist himself.

In the Originating Summons marked FHC / ABJ / CS / 232/2018, the plaintiff 8 issues for determination by the court, including: Having regards to the combined provisions of sections 79,116,118,132,153,160 (1) and 178 of the 1999 constitution as amended, the constitution read together with paragraph 15 (a) of the third schedule to the same constitution, whether the 3rd defendant (Independent National Electoral Commission) is not the only institution or body constitutionally vested with the powers and vires to organized, undertake and supervised elections to the offices of the president, the vice president of the federal republic of Nigeria, the Governor and deputy governor of a state, the membership of the Senate, the House of Representatives and the House of Assembly of each state of the federation, including fixing the sequence and dates of the elections to the said offices?

I remember looking at the report and realizing that there were all of these similar genes in all of these different animals and thinking: «Maybe a careful reading of the papers associated with the sequences most similar to mine will tell me something about my own gene.»

Machines copy DNA strands and modify them with fluorescent labels and other compounds to enable them to read DNA's sequence letters, or bases.

Given a large enough sample of DNA, the sequencing machines could not only read the lettering of a gene but could also distinguish a healthy gene from one with a harmful mutation — a disease gene.

«By reducing non-Y chromosome reads from our data with flow sorting and the RecoverY technique that we developed, and by using this combination of sequencing technologies, we were able to assemble the gorilla Y chromosome so that more than half of the sequence data was in chunks longer than about 100,000 bases in length,» said Medvedev.

In light of these findings and since tRNAs are repeat sequences themselves, the team had to devise a complex and stringent scheme with which they mapped the deep sequencing reads.

The key to their success was to generate long sequencing reads, producing an assembly with not many more scaffolds than C. krusei has chromosomes.

A rough draft is a sequence with 91 percent of the letters in the right place, each letter having been read and reread between five and seven times.

It scans a very broad area of the genome (508 genes and more than two million base pairs or letters of the genome, i.e.. A, T, C, and G) with high accuracy (each region of the genome is sequenced or «read» 60,000 times), yielding about 100 times more data than other sequencing approaches.

Massively parallel sequencing technologies, while increasing the speed, improving the accuracy, and reducing the cost of genome sequencing, typically produce only short stretches of sequences called «reads» After sequencing, the reads are pieced back together with genome assembly software.

With this quality control missing, the entire gene sequence is read as it spools through the ribosome.

The work on gorilla and other human genomes clearly demonstrates that large swathes of genetic variation can't be understood with the short sequence - read approaches.

By isolating strands of complementary DNA (cDNA) that fit together with mRNA, researchers can figure out what sequence was just translated into mRNA — that is, they can get a read on an expressed gene.

Paired - end reads were subsequently filtered to eliminate low - complexity sequences with a Lempel - Ziv - Welch (LZW) compression ratio below 0.4 [53], split into individual reads, classified by barcode, and stripped of any remaining primer sequences using BLASTN alignments (word size = 11, E-value = 1 × 10 − 5).

To assess low frequency disruption events, we conducted 454 deep sequencing on all 15 sites in both control CD4 + T cells and those treated with X4 - ZFNs, yielding approximately 7,500 — 26,000 reads per site in the ZFN - treated samples (Table S2).

Two papers by Langmead and team, Ultrafast and memory - efficient alignment of short DNA sequences to the human genome and Fast gapped - read alignment with Bowtie 2, have been cited in more than 12,000 scientific studies since 2009.

However, we previously reported that the bioinformatics algorithm would incorrectly assign a small fraction of sequenced DNA reads to chromosome Y in pregnancies with female fetuses.24 The percentage chromosome Y values of all studied pregnancies are shown in appendix 7 on bmj.com.

To avoid including reads sequenced from regions of the nuclear genome sharing high similarity with mitochondrial DNA (NUMTs), reads that did not map uniquely to the mitochondrial genome were discarded using SAMtools [32, 33].

After mapping, a custom bash function was used to remove reads with more than three mismatches compared to the mitochondrial DNA reference sequence; the revised Cambridge Reference Sequence (rCsequence; the revised Cambridge Reference Sequence (rCSequence (rCRS)[31].

While generating pileup files, reads and bases with a PHRED quality scores less than 30 (0.001 chance of sequencing error) were discarded from the dataset using the «-- q 30» and «-- Q 30» flags.

Here, we describe the results obtained from our current long read sequencing project of 100 Icelanders with Oxford Nanopore technology.

Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference.

An open source computer program for ordering short DNA sequence reads into long DNA fragments with the aid of the barcodes is also provided.

All variant loci were simulated with single - end reads using the genome sequence to build the reads, and for coding variants we simulated splice junctions and paired - end reads as well.

The ClonTracer library allows a researcher to label individual members of a starting population of cells with specifc, easily read sequences that can be used to measure their clonal abundance before and after a treatment.

Novel insertions of mobile elements into the sequenced genome are identified as clusters of reads that uniquely map to the reference genome with one arm and to ubiquitous sequence with the other arm.

We mapped sequencing reads to the Nvit1.0 assembly [15] using a TopHat2 [45] and Stampy [46], and then mapped reads which failed to align to the genome against the OGSv2 predicted transcriptome with bowtie2 [47] to improve mapping sensitivity (see methods for details).

For a total number of 131 cell line samples and 172 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines (Illumina, San Diego, CA, USA) using the standard Illumina RNA - seq protocol with a read length of 2x100 bases.

With longer (> 50 bp) fragment - end reads and / or paired - end libraries, it's possible to detect small insertion / deletion variants (indels) in next - gen sequencing data.

Complete Genomics does not produce assemblies (evidence intervals) for regions of the genome where the mapped reads are highly consistent with the reference sequence.

Early into our days of Illumina / Solexa sequencing, we observed a strange phenomenon in the data: lots of reads with identical start sites and orientations.

ChIP - Seq sequencing reads were mapped to the human genome (GRCh37 / hg19) using Bowtie2 with default parameters (v2.1.0, [27]-RRB-.

The resulting consensus sequences averaged 16,231 ± 455 bp, or 98.1 % of the complete mitochondrial genome, with the average number of reads per nucleotide position (fold - sequence coverage) ranging from 7.4 × to 117 × among the 9 individuals (Supplementary Data 1).

Base calling was performed with the machine learning algorithm Ibis [63] and overlapping read pairs obtained from paired - end sequencing runs were merged into single sequences.

During the pilot phase, the Project is analysing Illumina short - read sequence data on 2,512 samples from multiple locations in Africa and Asia, together with laboratory samples for benchmarking and methods development.

For whole genome sequencing of individual samples, we've used Maq with some success to map, assemble, and call variants from Illumina / Solexa reads.

Alexander Hoischen, Ph.D., Radboud University Medical Center «Medical genetics: Identification of hidden structural variants with long - read sequencing»

The long sequencing reads produced by Oxford Nanopore's platforms enable the assembly of genomes with superior contiguity compared to those produced by second generation technologies.

Reads are mapped to the previously sequenced XMRV genome corresponding to each of the samples, with the exception of reads from LNCaP, which are mapped to the 22Rv1 - associated genome (Genbank accession number FN692Reads are mapped to the previously sequenced XMRV genome corresponding to each of the samples, with the exception of reads from LNCaP, which are mapped to the 22Rv1 - associated genome (Genbank accession number FN692reads from LNCaP, which are mapped to the 22Rv1 - associated genome (Genbank accession number FN692043).

A consensus sequence based on mapped deep sequencing reads was generated for each of the prostate cancer XMRV genomes and used to correct errors in the previously published sequences, with the requirement of no ambiguity at each discrepant nucleotide position.

TFs with winged helix - turn - helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet «wing» into the adjacent minor groove.

Compared with short reads, the assemblies obtained from long - read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions.

Reads with a significant hit to the qnr PSSM and that aligned with at least 25 amino acids with 90 % sequence similarity to a known qnr gene were annotated as known.

We first assessed the sequencing quality of each platform with respect to distributing reads most evenly across the genome.

To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third - generation long - read sequencing.

Long - read sequencing technologies were launched a few years ago, and in contrast with short - read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes.