Identification and annotation of REs The data generated allowed the discovery of co-occurring histone modifications, CTCF binding, chromatin accessibility, and gene expression, which was used to identify regions with regulatory function and to link them with candidate target genes. We therefore first pr...
This library combines genomic and proteomic data from various databases (e.g. GENCODE, UCSC's reference genome, UniProt and pfam) into unified gene objects (currently only protein-coding genes). It allows you to infer the functional effects of genetic variations at the gene/protein-level....
Gene annotation is based on Ensembl genes (build 85). To match external gene IDs, ENSG ID is mapped to entrez ID yielding 35,808 genes which consist of 19,436 protein-coding genes, 9249 non-coding RNA, and other 7123 genes (e.g., pseudogenes, processed transcripts, immunoglobulin genes,...
To improve the cross-species comparison, we jointly use the similarity of coding sequences and of protein interactions. Our hybrid comparison method called graph alignment establishes a mapping between genes of two species [7] using a probabilistic scoring system based on evolutionary rates of sequenc...
were identified as microbial from the midgut contents and intact midgut libraries, respectively, and had highest scoring BLASTX alignments to microbial protein coding genes present in the NCBI non-redundant protein database at an e-value of 1e-5 or lower, a minimum alignment length of 15 amino...
CRISPRO pipeline.aDense mutagenesis of protein coding sequence by pooled CRISPR screening approach. Single guide RNAs target every possible PAM within the coding sequence of a set of genes. Guide RNAs are mapped to the two amino acids closest to the nuclease (e.g., Cas9) cleavage site.bOver...
The 47 NRSs have an apparently lower P-value, and most of which have a higher frequency in heat-resistant pigs (Fig. 5A). This region might have experienced strong selection during their adaptation to tropical environments. There are 59 known protein coding genes located in the 11.6 Mb ...
Protein Experimental Models Kits Other Keywords No genome sequencing project is complete without structural and functional annotation. Gene models and functional predictions for these models can be obtained relatively easily using computational methods, but they are prone to errors. We describe ...
Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-spec
coding efficiency and error control, as a smaller genetic space is used compared to a monomeric protein of a similar size. From a purely physical perspective, the formation of a homomeric complex can potentially lead to higher stability, as a larger proportion of protein surface area is buried,...