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

This article mainly introduces the use of LGC tools, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

The Beijing Genome Research Institute of the Chinese Academy of Sciences has set up the domestic big data Center BIGD, which has massive computing resources and more than 5000 CPU,8PB storage. With the help of huge computing resources, it stores all kinds of combinatorial data generated by high-throughput sequencing, and integrates various analysis software to form an application system for combinatorial data integration and mining.

The LGC tool to be introduced today is a lncRNA prediction software integrated into BIGD. The source code is stored in the BioCode` database provided by BIGD at the following URL

Http://bigd.big.ac.cn/biocode/tools/BT000004

An online version is also available at the following URL

Http://bigd.big.ac.cn/lgc

Online tools support input files in fasta, bed and gtf formats, as shown below

For bed and gtf formats, you also need to specify a version of the genome, which currently supports the following

Human (hg38, GRCh48)

Human (hg19, GRCh47)

Mouse (GRCm38/mm10)

Mouse (NCBI Build 37/mm9)

Fly (dm3, BDGP Release 5)

Zebrafish (Zv9/danRer7)

The installation of the local version is also very simple, using the python language for development, only need to download the source code, it is important to note that the software relies on the biopython module. The local version is used as follows

Python lgc-1.0.py transcript.fa output.txt

The first parameter is the fasta sequence corresponding to the transcript, and the second parameter is the output file, which can be divided into

The two parts, the comment lines that begin with #, explain the meaning of each column in the text, as follows

The text is as follows

The Coding lable column identifies the protein coding of the transcript.

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