Intro Run Help Download Related Links About

Tool / Method Download Web server Instruction
CPC (2007)* 0.9-r2 Run CPC Documents
PhyloCSF (2011)* Apr 24 2013 - README
CPAT (2013)* v1.2.4 Run CPAT Documentation
CNCI (2013) v2 - README
PLEK (2014) v1.2 - Tutorial
lncRNA-MFDL (2015)** - Expired -
LncRNA-ID (2015)** scripts - -
lncRScan-SVM (2015) v1.0.1 - README
LncRNApred (2016)** - Expired -
lncScore (2016) v1.0.0 - Manual
Lncident (2016) v1.3.3 Run Lncident Manual
COME (2017) v1 Run COME README
LncFinder v1.1.0 Run LncFinder Manual
Most of the tools listed in table have been compared in our article (PMID: 28042575). Click here for more information.

* The tools listed in the table can all be used to predict lncRNA. But please note that CPC and CPAT are originally designed to assess coding potential; PhyloCSF is initially developed to distinguish protein coding and non-coding regions, whereas other tools are tailored to lncRNA identification.
** LncRNA-ID only provides part of script. lncRNA-MFDL and LncRNApred only have web interfaces, and the links of their web servers are not available when we conduct our research (24 Mar. 2017).
Database Description
RefSeq NCBI Reference Sequence Database. A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
GENCODE The GENCODE project produces high quality reference gene annotation and experimental validation for human and mouse genomes.
Ensembl Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
UCSC Genome Browser An interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
RNAdb A comprehensive mammalian noncoding RNA database.
NONCODE NONCODE is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Now, there are 16 species in NONCODE 2016.
ncRNAdb This database is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell.
lncRNAdb The Reference Database For Functional Long Noncoding RNAs.
RNAcentral A database that collates and integrates information from an international consortium of established RNA sequence databases.
LNCipedia A comprehensive compendium of human long non-coding RNAs. The database is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria.
GreeNC A Wiki-database of plant lncRNAs.
NRED ncRNA Expression Database (NRED) integrates annotated expression data from various sources.
LncRNADisease LncRNADisease database integrated more than 1000 lncRNA-disease entries and 475 lncRNA interaction entries, including 321 lncRNAs and 221 diseases from ~500 publications.
Items Description
lncRNA Blog lncRNA research and industry news.
Related Research from Nature Latest research and reviews from Nature.