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NONCODE v2.0: decoding the non-coding.

He S, Liu C, Skogerbø G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R - Nucleic Acids Res. (2007)

Bottom Line: The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs).Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms.In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn.

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Related in: MedlinePlus

Links between the NONCODE ncRNA annotations, the Genome Browser and NCBI. (A) The NONCODE database window with ncRNA annotations. (B) The corresponding NCBI annotation. (C) The corresponding Genome Browser window. (D) The link from Genome Browser to NONCODE.
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Figure 1: Links between the NONCODE ncRNA annotations, the Genome Browser and NCBI. (A) The NONCODE database window with ncRNA annotations. (B) The corresponding NCBI annotation. (C) The corresponding Genome Browser window. (D) The link from Genome Browser to NONCODE.

Mentions: All sequences can be directly downloaded from the webpage. Sequences can be searched using accession numbers found in GenBank, name, traditional class, PfClass, organism and UniqID in NONCODE. In addition to access to NONCODE database records, search results are also linked to full GenBank entries (Figure 1). In the current version of the database, we also included the online BLAST service (NCBI wwwBLAST version 2.2.17) which allows sequence similarity searches against the entire NONCODE v2.0 database.Figure 1.


NONCODE v2.0: decoding the non-coding.

He S, Liu C, Skogerbø G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R - Nucleic Acids Res. (2007)

Links between the NONCODE ncRNA annotations, the Genome Browser and NCBI. (A) The NONCODE database window with ncRNA annotations. (B) The corresponding NCBI annotation. (C) The corresponding Genome Browser window. (D) The link from Genome Browser to NONCODE.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238973&req=5

Figure 1: Links between the NONCODE ncRNA annotations, the Genome Browser and NCBI. (A) The NONCODE database window with ncRNA annotations. (B) The corresponding NCBI annotation. (C) The corresponding Genome Browser window. (D) The link from Genome Browser to NONCODE.
Mentions: All sequences can be directly downloaded from the webpage. Sequences can be searched using accession numbers found in GenBank, name, traditional class, PfClass, organism and UniqID in NONCODE. In addition to access to NONCODE database records, search results are also linked to full GenBank entries (Figure 1). In the current version of the database, we also included the online BLAST service (NCBI wwwBLAST version 2.2.17) which allows sequence similarity searches against the entire NONCODE v2.0 database.Figure 1.

Bottom Line: The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs).Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms.In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

ABSTRACT
The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn.

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Related in: MedlinePlus