UCSC Genome Bioinformatics: Frequently Asked Questions (2023)

FAQs

What is the difference between UCSC and Ensembl Genome Browser? ›

Ensembl uses a one-based coordinate system, whereas UCSC uses a zero-based coordinate system. Ensembl uses the most recently updated human genome housed at the GRC. This current major assembly release is called GRCh38. NCBI and UCSC use the same genome.

It allows control over the style of sequencing displayed (e.g., genomic coordinates, sequences, gaps etc.). It can also display a percentage based track to show a researcher if a particular genetic element is more prevalent in the specified area.

What is the difference between GENCODE GTF and Ensembl GTF? The gene annotation is the same in both files. The only exception is that the genes which are common to the human chromosome X and Y PAR regions can be found twice in the GENCODE GTF, while they are shown only for chromosome X in the Ensembl file.

The basic difference is that RefSeq is a collection of non-redundant, curated mRNA models, whereas Ensembl is a database containing more gene models from multiple sources, mapped to the reference genome. That question has more to do with Entrez Gene than Entrez RefSeq.

Click the entry for the gene in the RefSeq or Known Genes track, then click the Genomic Sequence link. Alternatively, you can click the DNA link in the top menu bar of the Genome Browser tracks window to access options for displaying the sequence.

Genome browsers are invaluable for viewing and interpreting the many different types of data that can be anchored to genomic positions. These include variation, transcription, the many types regulatory data such as methylation and transcription factor binding, and disease associations.

Gene Editing

Homing endonucleases have not achieved widespread adoption as tools for genome engineering. One reason for this is that while many modified homing endonucleases with different DNA-binding specificities have been created, they lack the modular DNA-binding domain architecture found in ZF or TALE proteins.

GRCh38: What's the Difference? Both, GRCh37 and GRCh38 are human genome assemblies by the Genome Reference Consortium (GRC). GRCh38 (also called “build 38”) was released four years after the GRCh37 release in 2009, so it can be viewed as a version with updated annotations to the earlier assembly.

What is the difference between GenBank and RefSeq sequences? ›

GenBank sequence records are owned by the original submitter and cannot be altered by a third party. RefSeq sequences are not part of the INSDC but are derived from INSDC sequences to provide non-redundant curated data representing our current knowledge of known genes.

GRCh38 is an improved representation of the human genome compared to GRCh37, where many gaps were closed, sequencing errors corrected and centromere sequences modelled. For the state-of-the-art of the human genome and its annotation, go to GRCh38.

RefSeq transcript and protein records for a subset of organisms, primarily mammals, are curated by NCBI staff. Curation is an ongoing process and some records have not been reviewed yet; the curation status is indicated on the RefSeq record in the COMMENT block.

GRO-Seq is a derivative of RNA-Seq that aims to measure rates of transcript (instead of steady state RNA levels) by directly measuring nascent RNA production. Transcription is halted, nuclei are isolated, labeled nucleotides are added back, and transcription briefly restarted resulting in labeled RNA molecules.

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation.

There are four main types of genome-wide repeat, called LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), LTR (long terminal repeat) elements and DNA transposons. Examples of each type are seen in this short segment of the genome.

The Australian lungfish has the largest genome of any animal so far sequenced. Siegfried Schloissnig at the Research Institute of Molecular Pathology in Austria and his colleagues have found that the lungfish's genome is 43 billion base pairs long, which is around 14 times larger than the human genome.

All of Us Research Program Makes Nearly 250,000 Whole Genome Sequences Available to Advance Precision Medicine. All of Us genomic dataset is world's largest and most diverse dataset of its kind, paving the way to advance precision medicine.

Here, pseudogenes are defined as genomic sequences that are similar to known genes but exhibit various inactivating disablements (e.g. premature stop codons or frameshifts) in their putative protein-coding regions and are flagged as either recently-processed or non-processed.

What tool do we use from the UCSC genome browser? ›

The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a UCSC Genome Browser mirror.

After a genome has been sequenced, assembled and annotated it needs to be shared in a format that is easily and freely accessible to all. This can be done via a database called a genome browser.

Three major genome browsers are freely accessible online — the University of California, Santa Cruz (UCSC) Genome Browser, the Wellcome Trust Sanger Institute (WTSI)/European Bioinformatics Institute (EBI) Ensembl browser and the National Center for Biotechnology Information (NCBI) MapViewer.

Whole Genome Sequencing provides the most accurate and powerful look at DNA traits related to health, disease, fitness, and nutrition. Whole-genome sequencing (WGS) is by far the most powerful form of DNA sequencing available on the market.

CRISPR/Cas9 is the most widely used genome editor and is a powerful tool for understanding gene function. Because CRISPR/Cas9 is an RNA-based system, it can be more efficiently and easily modified than the protein-based approaches and allows for targeting of multiple sites.

The 1000 Genome Browser is an interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project.

DNA replacement in human embryos (germline genome therapy) The most controversial usage of CRISPR-Cas9 is the modification of human embryo DNA, or, in other words, its use for germline genome therapy.

CRISPR/Cas9 – a specific, efficient and versatile gene-editing technology we can harness to modify, delete or correct precise regions of our DNA. Dr. Emmanuelle Charpentier, one of our scientific founders, co-invented CRISPR/Cas9 gene editing.

CRISPR-Cas9 was adapted from a naturally occurring genome editing system that bacteria use as an immune defense. When infected with viruses, bacteria capture small pieces of the viruses' DNA and insert them into their own DNA in a particular pattern to create segments known as CRISPR arrays.

Here, the improved reference genome (HG38) increased the number of SNVs identified from identical sequencing data, suggesting that genetic variants missed by using HG19 could be identified using HG38. Therefore, we again recommend the newer version (HG38) for sequencing data analysis aimed at variant calling.

Can you have two humans with exactly the same genome? ›

Theoretically, same-sex siblings could be created with the same selection of chromosomes, but the odds of this happening would be one in 246 or about 70 trillion. In fact, it's even less likely than that.

Every person's genome is around 99.9% the same as everyone else's, but that 0.1% equates to around 3 million differences. Others can influence our susceptibility to develop a disease. We can now sequence and analyse genomic information to inform healthcare, helping to better diagnose, treat and even prevent disease.

Two methods, whole exome sequencing and whole genome sequencing, are increasingly used in healthcare and research to identify genetic variations; both methods rely on new technologies that allow rapid sequencing of large amounts of DNA. These approaches are known as next-generation sequencing (or next-gen sequencing).

Searches with protein sequences (BLASTP, FASTP, SSEARCH,) or translated DNA sequences (BLASTX, FASTX) are preferred because they are 5–10-fold more sensitive than DNA:DNA sequence comparison.

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. Scaffolds are composed of contigs and gaps. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level.

GWAS is based on the common disease-common variant hypothesis, and could provide information on how common genetic variability confers risk for the common diseases (2). While for rare Mendelian disorders, NGS could pinpoint novel genes that contain mutations underlying the phenotype.

WGS aims to analyze the whole genome of a single bacterial colony, while amplicon-based marker gene sequencing (e.g., 16S/ITS) or shotgun metagenomics focuses on microbial communities within a sample, usually without culture [9,10].

While Ensembl gene models are annotated directly on the reference genome, RefSeq annotates on mRNA sequences. Due to sequence differences between the reference genomes and individual mRNAs, some of the RefSeq mRNAs may not map perfectly to the reference genome.

A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

Can you use trizol for RNA-Seq? ›

We do not recommend the use of Trizol alone for total RNA isolation, as the use of Trizol often results in samples that are contaminated by proteins and organics which can inhibit the library making process.

What is the difference between RNA-Seq and transcriptomics? Transcriptomics broadly refers to the study of RNA related to its expression levels, function, structure, and regulation. RNA-Seq is more specific and refers to the technique to study both the sequence and quantity of RNA.

Illumina sequencers tend to be high accuracy with a read accuracy of >99.9% while Oxford Nanopore provides sequencers with a read accuracy of between 87% and 98%⁴. Of course, the cost usually plays an important role in any purchasing decision.

The RefSeq collection includes complete or incomplete genome sequences, transcripts and proteins. Genomic sequence records are added when whole genome submissions are submitted to GenBank and are updated as those genome sequencing projects submit updates.

Viral genomes exhibit extraordinary diversity with respect to nucleic acid type, size, complexity, and the information transfer pathways they follow. Thus, viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long.

RefSeq Gene Fnip1

Description: Mus musculus folliculin interacting protein 1 (Fnip1), mRNA.

Ensembl provides a genome browser that acts as a single point of access to annotated genomes for mainly vertebrate species (Video 1 and Figure 2). Information about genes, transcripts and further annotation can be retrieved at the genome, gene and protein level.

The Genome Browser in the Cloud (GBiC) program is a convenient tool that automates the setup of a UCSC Genome Browser mirror.

While Ensembl gene models are annotated directly on the reference genome, RefSeq annotates on mRNA sequences. Due to sequence differences between the reference genomes and individual mRNAs, some of the RefSeq mRNAs may not map perfectly to the reference genome.

Genome Browser annotation tracks are based on files in line-oriented format. Each line in the file defines a display characteristic for the track or defines a data item within the track. Annotation files contain three types of lines: browser lines, track lines, and data lines.

What kind of database is Ensembl? ›

Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms.

The bigWig format is useful for dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created from wiggle (wig) type files using the program wigToBigWig . Alternatively, bigWig files can be created from bedGraph files, using the program bedGraphToBigWig .

MMDB. NCBI has upgraded both the MMDB (Molecular Modeling Database) and GenBank sequence record tools so that they can process the complete set of Protein Data Bank (PDB) molecular structure data.

GenBank sequence records are owned by the original submitter and cannot be altered by a third party. RefSeq sequences are not part of the INSDC but are derived from INSDC sequences to provide non-redundant curated data representing our current knowledge of known genes.

For read-counting methods, such as gene expression profiling, the digital nature of NGS allows a virtually unlimited dynamic range. RNA-Seq quantifies individual sequence reads aligned to a reference sequence, producing absolute rather than relative expression values.

The UCSC genome browser uses both systems and refer to the base coordinate system as “one-based, fully-closed” (used in the UCSC genome browser display) and interbase coordinate system as “zero-based, half-open” (used in their tools and file formats).

In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription. In situations where no intron is visible (e.g. single-exon genes, extremely zoomed-in displays), the arrowheads are displayed on the exon block itself.