Sentences with phrase «gene models»

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

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

Sequence of the extended gene models for the VR repertoire.

Overall, we can only detect measurable expression for 58 % of OGSv2 gene models, but we detect measurable expression for all 101 genes encoding signaling proteins.

We found a surprisingly high number of novel transcripts that map some distance away from known genes, and encode consistent multi-exonic gene models.

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

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.

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).

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

Seqping: gene prediction pipeline for plant genomes using self - training gene models and transcriptomic data

The task of assembling RNA - Seq short reads into gene models is not trivial; in particular, we needed to overcome the issues of transcript contiguity and fragmentation.

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.

The ENSEMBL gene models are also included.

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.

Data shown for Olfr1420 as an example; in red is the Ensembl gene model, with the UTR regions in grey, and in black the models produced by Cufflinks.

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

We investigated cases of alternative splicing by retaining all the multi-exonic receptor gene models and counted the number of alternative isoforms produced.

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.

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).

Extended gene models for the OR repertoire.

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.

The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes.

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.

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.

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

These are typically determined from DNA sequence data alone based on the known genetic code and gene models.

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

As a complement and extension of our new homology - based immune annotation of the OGSv2 gene models, we characterized the infection - induced transcriptome in N. vitripennis to identify genes up - regulated by infection.

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.