Shulou(Shulou.com)06/01 Report--

This article will explain in detail what is the use of gencode database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

For human and mice, the corresponding gene annotation information is saved in NCBI, Ensembl and other databases, and the information sources and credibility in different databases are different. Gencode integrates the information in HAVANA and Ensembl databases and verifies it by experimental means to build a high-quality annotation information database. The web address is as follows

Https://www.gencodegenes.org/

The official website provides files in GTF and GFF3 formats for download, as shown below

Each type of file provides three areas

CHR

ALL

PRI

For the genome, it includes chromsome,unplaced_scaffold, alt_scaffold, patch and other sequences, and there are corresponding genes on these sequences. CHR refers to information at the chromosome level, including chromosomes and mitochondria in the nucleus; ALL includes all sequences, and PRI contains only information on chromosomes and unplaced_scaffold sequences. Official recommendation, use CHR-level information.

Level is used to express the credibility of the annotation information in the file, including a total of 3 level.

Level1 represents reliable annotation information, which is supported by direct experimental evidence; level2 represents manual proofreading, taking the same annotation information in HAVANA and Ensembl annotation information; level3 refers to software annotation information, which is usually inconsistent with HAVANA in Ensemble.

If you want to get more reliable comment information, you can filter it according to level and select only 1 and 2 levels of comment information.

The total number of genes and transcripts contained in the document is as follows

1. Human

2. Mouse

In the document, the type information of the gene or transcript is given, which is explained as follows

Protein_coding

Protein coding gene

LincRNA

Long-stranded noncoding RNA located in intergenic region

Non_coding

Non-coding RNA confirmed in the literature

This is the end of this article on "what is the use of gencode database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.