« Home « Kết quả tìm kiếm

Gene annotations

Tìm thấy 13+ kết quả cho từ khóa "Gene annotations"

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

tailieu.vn

Results: Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%..

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations

tailieu.vn

Input layer This allows the user to upload a gene struc- ture annotation set, genome assembly and transcript file (optional) for analysis. Users also have the option to benchmark the quality of the uploaded gene annotations.

The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes

tailieu.vn

Specifically, pre- dicted open reading frames (ORFs) in assembled RNA- seq transcripts [27] as well as protein sequences of the community-curated P. gene annotations [9]. annotation accuracy occurs already within the same nematode family, I reevaluated the BUSCO complete- ness of the gene annotations only inferred from hom- ology data (Fig. Moreover, the evaluation of the contribu- tion of homology-inferred vs.

Enhanced genome assembly and a new official gene set for Tribolium castaneum

tailieu.vn

PI, RMW, EZ performed the orthology assignment of the new gene set and drafted the manuscript. CL determined the termini of the gene annotations. JS, PK, JU, SD, GO, YH, JS, MS, SL, AM, NP, DG, TH, JS, IMVJ, KAP performed the manual quality control of the new gene set. All authors consent with the publication of this version of the manuscript.

Conserved associations between Gquadruplex-forming DNA motifs and virulence gene families in malaria parasites

tailieu.vn

Since the gene annotations in the v.44 assem- blies did not specify particular var classes (e.g. upsB-type var genes were defined as those at the far ends of the chromo- somes and transcribed inwards (with the 5′ UTR nearest the telomere).. Statistical analysis of the co-distribution of PQSs and multigene families. For each species, a list of PQS-associated genes was compiled from the QGRS Mapper and G4 Hunter data- sets.

ManiNetCluster: A novel manifold learning approach to reveal the functional links between gene networks

tailieu.vn

These ontologies (and gene annotations where they exist), together with the interactions with the rest of the module, suggest the possibility of a hierarchical gene/protein regulatory network, with these genes puta- tively imposing some aspect of regulation upon the rest of the module.

Millefy: Visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

tailieu.vn

For example, read coverage overlapped with gene annotations can confirm known and reveal novel exon-intron struc- tures. Moreover, read coverage overlapped with enhancer annotations can be interpreted as eRNA expression [6].. Using Millefy, single-cell read coverage can be compared. 2 Millefy visualization of read coverage at the Sox17 locus. The top heat map shows single-cell read coverage.

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

tailieu.vn

Nevertheless, more than 3000 intergenic loci, relative to gene annotations in the mouse, had a conserved open chromatin signature in at least one tissue in all three spe- cies. ATAC-seq library construction and sequencing. A modified ATAC-seq protocol compatible with cryo- preserved tissue samples was employed [62].

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

tailieu.vn

To assess the nucleotide diversity of single-domain heavy-chain IG genes in our data, we first downloaded the scaffold.fasta.gz (Ming et al.’s [12] Camelus ferus genome assembly) and IGH.gff (heavy-chain immuno- globulin gene annotations) from https://figshare.com/arti- cles/Data_from_Chromosome-level_assembly_of_wild_Bac- trian_camel_genome_reveals_organization_of_immune_.

PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis

tailieu.vn

In this study, all the the ToxB loci (585 bp) identified have Table 3 Ptr isolate DW5 ToxB subtelomeric gene locations, chromosomes relative to M4 and sequence identity to DW7 ToxB cloned sequence. 2 Alternating strand positions of ToxB loci Ptr isolate DW5 in contigs 15, 16 and 18. ToxB loci are shown as blue arrow on the forward strand and green on the reverse strand. DW5 contigs 15, 16 and 18 are represented on the horizontal axis with gene annotations below (yellow boxes).

Comparative genomic analysis of eutherian fibroblast growth factor genes

tailieu.vn

The protocol used guidelines of human gene nomenclature [61] and guidelines of mouse gene nomenclature [62] in updated eutherian FGF gene classification and nomenclature.. Third, the protocol used new genomics tests of contiguity of eutherian public genomic sequences in eutherian FGF gene annotations.

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

tailieu.vn

Sequence align- ment, gene annotations and sequencing coverage indi- cated two versions of the ScI contigs: one with and one without the gene UIP3 (Fig. In addition to the increased coverage of the right arm of ScI, the left arm of ScXIV showed decreased sequencing coverage up until the ~ 561 Kbp position.. Together, these results suggest that the left arm of one copy of ScXIV was replaced with an additional copy of the right arm of ScI (Fig.

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

tailieu.vn

When added to existing cala total 59,377 unam- biguous calls accounting for 81% of the gene annotations were made (Additional File 1).. The identification of the a sub-genome donor. The A sub-genome donor was identified using a unified genomics approach, and the absence of the B sub-genome donor was identified in the largest set of species to date.. According to a study by Zhang et al. So a rethinking of the labeling of ancestral genomes of E.

Using multiple reference genomes to identify and resolve annotation inconsistencies

tailieu.vn

On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3 – 5% of gene models across annotations. Conclusions: Split-gene misannotations occur at appreciable frequency in maize annotations. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.. Keywords: Annotation, Genome assembly, Maize, Split-gene.

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and conditionspecificity

tailieu.vn

The significant convergence of mutated features on functional annotations contextualized the targets of the. coli K-12 MG1655 [31]. Similar to the U00096.2 E.. Overall, 53% of the mutations to glpK have effects that could dis- able inhibition by FBP (Fig. The presence of mutations to either of these targets was in- versely correlated with the other (Fig. A large proportion of the mutations to the cyaA gene had a disruptive effect.

Human gene expression variability and its dependence on methylation and aging

tailieu.vn

The breast, cerebellum, and frontal cortex Hyper-Variable probe-mapped gene sets were commonly enriched for regulation of tissue remodeling, inflammatory responses, and responses to inorganic substances. Of note, many of the enriched GO annotations of the Hyper- Variable genes are involved in signalling pathways.. Table 3 Top 5 common and tissue-specific REVIGO GO annotations in the Hyper-Variable and Hypo-Variable probe mapped gene sets of breast, cerebellum, and frontal cortex tissues.

Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

tailieu.vn

Add- itional file 11) and compared the GO terms with the functional annotations of the significantly enriched Fg motifs. We found that the functional annotations of 27 of the 49 modules (55%) matched in the enriched TFBS and GO enrichment (Fig.

Intron and gene size expansion during nervous system evolution

tailieu.vn

Branch lengths were obtained from TimeTree.org [22], and scale bar shows 100 million years. b Boxplots of median gene length of long genes of each genome in kilobases aggregated by clade. This extends similar analyses by Lynch et al. Gene start posi- tions were subtracted from gene end positions to obtain a measure of gene length for each gene that excludes 5′. The branch lengths obtained from TimeTree.org [22]. were combined with gene length annotations using the.

Species and population specific gene expression in blood transcriptomes of marine turtles

tailieu.vn

We used Blast2GO (v to functionally an- notate the de novo green turtle transcriptome, and linked annotations to the other species-specific tran- scriptomes via orthogroups identified as described above. Gene expression analyses between species. functional enrichment between green turtle foraging aggregations. differential expression analyses between the three green turtle foraging aggregations using the R packages edgeR and limma [89, 100].

Insights into the skin of caecilian amphibians from gene expression profiles

tailieu.vn

SPF proteins identified here in caecilians belong to the same gene fam- ily of sodefrin that is a courtship pheromone produced in the gonads of male salamanders [43, 44]. Several of the AMP annotations were previously known only from other animal groups.. A greater prevalence of candidate AMP expression in posterior skin samples is consistent with the higher abundance of toxin secreting granular glands in the pos- terior body region of caecilians [26]..