Sentences with phrase «ensembl gene model»

The MAKER - P annotation pipeline combined evidence - based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence.

Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers.

Two of the genes modeled in this study, Pten and Nkx2.1, have been extensively studied in lung cancer.

In order to use these data sets to build gene models we created an analysis pipeline consisting of five steps:

Reads were mapped to the S. viridis A10.1 reference genome (phytozome.jgi.doe.gov; v1.1) using TopHat2 (v2.1.0) and an a priori set of 35,214 gene models.

This section describes the wheat genome assemblies available, gene models, using EnsemblPlants to access wheat data, accessing wheat expression data, finding variation data and finding the wheat orthologue of genes from other species.

RNA - seq reads from wild - type and mutant libraries were mapped to the S. viridis reference genome (v1) and annotated gene models used to quantify transcript abundances (Supplemental Data Set 3).

These improvements in contiguity and reduction of gaps had a large impact on the quality of the gene models.

To better understand the evolutionary history of immune genes in Nasonia, we estimated gene age for all OGSv2 gene models.

First, we add all antimicrobial peptides identified by a previous computational screen [35], filtered to remove cases where gene models were removed during a subsequent annotation or NCBI gene models could not be associated with OGS 2.0 gene models.

In both cases, the results are based on the same set of blastp searches, in which we blasted each Nasonia gene against the predicted proteomes of 30 additional species, including 12 additional Hymenoptera genomes, 6 Dipteran genomes, 5 additional insect genomes, 2 additional non-insect arthopod genomes, and 5 non-arthropod outgroup genomes (see Table S4 for the full list, including gene model versions and data sources).

DNA Subway ties together key bioinformatics tools and databases to assemble gene models, investigate genomes, work with phylogenetic trees and analyze DNA barcodes.

Most successfully mapped reads (84.0 % for the uninfected library, 86.5 % for the infected library) overlap a gene model, suggesting we are not missing large numbers of transcribed but unannotated genomic regions.

While it is not straightforward to directly compare the immune repertoire reported here with previous reports that have used different underlying gene models [15], [34], we do note that our inference about the number and identity of signaling components is consistent with previous annotations [15], [34], while our inference about recognition and effectors tends to reflect greater, albeit still relatively minor, differences.

Out of 24,389 OGSv2 gene models, we did not detect any expression in either sample for 2,950 genes and filter an additional 7,289 genes because of low average expression (leaving little or no power to infer differential regulation for these genes).

The reconstructed gene models for VR genes based on the VNO RNAseq dataset, provided in GTF format.

The generation of RNAseq data for a majority of ORs and VRs enabled us to obtain new, significantly extended gene models.

The D. plexippus genomic scaffolds and gene model information (OGS1) were downloaded from MonarchBase (http://monarchbase.umassmed.edu/home.html).

We therefore assessed whether our new gene models will help resolve this by determining the proportion of each gene sequence that is unique in the genome.

All but one (Olfr332) of these gene models are reported in Ensembl and classified as protein coding (Dataset S8).

When we compare the complete gene models we have reconstructed with those currently annotated, both the amount of the receptor transcript sequence, and the proportion that is unique between receptors increases substantially.

We find a large increase in the proportion of unique sequence in our new extended V1R (P < 0.0001, Mann Whitney test) and V2R gene models (P < 0.0001, Mann Whitney test); a more modest increase is apparent in OR genes (P = 0.044, Mann Whitney test; Figure 7D).

Sequence of the extended gene models for the VR repertoire.

The ENSEMBL gene models are also included.

Extended gene models for the OR repertoire.

Extended gene models for the VR repertoire.

Ad hoc perl scripts were used to further refine the gene models produced for VR and OR genes, deleting those predictions that fuse adjacent receptor genes or that are antisense to the annotated gene.

(A — B) An example of new gene models generated for Olfr168 (A) and Vmn1r34 (B) are shown in black.

We next compared the 5 ′ ends of the OR gene models reconstructed here using Cufflinks, to the proposed transcription start sites (TSS) reported by Plessy et al. (2012) using nanoCAGE [29].

In black are Lcn16 and Lcn17 gene models, where boxes correspond to the exons.

This curation effort has resulted in several improvements to the gene set including the addition of UTRs to gene models, correction of gene boundaries and exons, and the discovery of nearly 650 new genes.

We sequenced at sufficient depth to produce new, extended receptor gene models for 913 (73.1 %) OR and 246 (45.9 %) VR genes (the models and their sequences are provided in Datasets S4, S5, S6, S7).

The median length of Ensembl V2R genes is 2,559 nt, while for the V2R reconstructed gene models it is 2,912 nt (Figure 7C).

The scaffold positions along scaffold3899 are shown above the gene models with the region amplified by the PCR is highlighted by the box.

The reconstructed gene models for OR genes based on the OM RNAseq dataset, provided in GTF format.

Sequence of the extended gene models for the OR repertoire.

The sequences of the reconstructed gene models for OR genes in FASTA format.

As a result, reference gene collections remain incomplete - many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs).

Everts (2000) suggested a major gene model for fragmented coronoid process, which is one form of a growth disorder in the elbow joint, but approximately 80 % of the dog genome was excluded as a candidate region in a search of markers, under a hypothesis of a recessive inheritance.

Goodness - of - fit of the polygenic and major gene models were compared using the residual sums - of - squares (SS) as in Palmer et al. (2001).

Not exact matches

Our study in an animal model found that influenza infection leads to an increase in the expression of muscle - degrading genes and a decrease in expression of muscle - building genes in skeletal muscles in the legs.

Essentially the model reproduces the inner workings of all of the proteins within the organism and allows scientists to see everything from how cells interact with each other to the functions of genes in a larger context that had not been previously understood.

Analyst Gene Munster is predicting Tesla will likely miss its Model 3 production targets, Bloomberg reports.

In many animal model systems, for example, the precise genes involved in sexual partner selection have been identified, and their neuro - biochemical pathways have been worked out in great detail.

He continued to value his relations with colleagues at Yale like George Lindbeck, David Kelsey, Wayne Meeks and Gene Outka, and he eagerly welcomed the 1984 publication of Lindbeck's Nature of Doctrine, with its model of a «postliberal theology,» for which Frei's work is the paradigm.

The best model of what's happening is constrained randomness — random mutation constrained to a sort of space of all possible functioning variations of the gene.

This dataset contains millions of genomic sequences from a diverse set of rice varieties that, when combined with phenotyping observations, gene expression, and other information, provides an important step in establishing gene - trait associations, building predictive models, and applying these models to breeding.

We've developed a range of tools and techniques to answer today's challenges and plan for the future, including gene technology, digital modelling and region - specific strategies.

Simulating the yield impacts of organ - level quantitative trait loci associated with drought response in maize: A «gene - to - phenotype» modeling approach.

The disruption of prenatal cellular activity in zebra fish, which share 80 percent of their genes with humans and are considered a good model for studying human brain development, seemed to result in hyperactivity, according to the Canadian study, which was published Monday in the Proceedings of the National Academy of Sciences.