Table 1 Summary table of the most popular databases and tools storing information about micro and long ncRNAs

NONCODE

Contains a total of 487.164 lncRNA transcripts and 324.646 lncRNAs genes for 16 different species and allows searching sequences, expression, orthologs, functions and diseases related, to a given input gene or transcript.

http://www.noncode.org/

PA

(+) High Number of sequences

(+) 17 different species

(+) Disease Association

(+) Simple Analysis

(+) High level of manual

curation

LncRNAMap

Is a web resource for studying lncRNAs in the human genome and currently contains 23.355 lncRNAs with sequences retrieved from Ensembl 65 (GRCH37)

http://lncrnamap.mbc.nctu.edu.tw/php/

PA

(−) No Analytic potential

(−) No recent updates

LNCipedia

Includes 127.802 human lncRNAs transcripts, provides sequence, annotations and manually curated lncRNA articles

https://lncipedia.org/

PA

(+) Recent Web Interface

(+) API Interface for data integration

(+) Submission of novel sequences

LncRNADisease

Integrates approximately 1000 lncRNAs-to-disease associations, including cancer, obtained using lncRNA -disease prediction tools that compare lncRNA genomic location with the closer gene

http://www.cuilab.cn/lncrnadisease

PA

(+) Prediction of associations on the basis of user-provided sequences

(+) High level of manual curation

(+) Submission of novel sequences

(−) Web Interface Obsolete

lncRNAdb

Is a database of long-noncoding RNAs in eukaryotes storing both raw data about sequence as well as other referenced information such as structural information, genomic context, levels of expression, and functional information

https://rnacentral.org/expert-database/lncrnadb

PA

(−) Limited number of sequences

(+) Extensive annotation and biological knowledge is provided

(+) High level of manual curation

LncRNA2Target

Expression profiling analysis following lncRNA Knockdown or Overexpression

http://123.59.132.21/lncrna2target/

PA

(−) Limited Scope

(−) Obsolete web interface

NRED

Provides comprehensive information on lncRNAs and lncRNA expression data from microarray and In situ Hybridization data

https://www.hsls.pitt.edu/obrc/index.php?page=URL1237993821

PA

(−) Limited Scope

(−) Obsolete web interface

GENCODE

Contains ncRNA gene annotations in .gtf format and ncRNA transcript sequences in .fasta format. Its goal is the investigation of gene features based on biological evidence

https://www.gencodegenes.org/

PA

(−) Limited access (only by FTP)

(−) Limited Query Capabilities

ENCORI

Is focused on miRNA-target interaction, including miRNA-lncRNA and protein-lncRNA interaction data

http://starbase.sysu.edu.cn/

Upon Request

(−) No Simple Access

NPInter

Stores functional interactions between ncRNAs and other molecules (DNAs, RNAs and proteins) and is regularly updated with novel interactions coming from manual curation of literature, high throughput screening and in silico predictions.

https://omictools.com/npinter-tool

PA

(+) Regular Updating

(+) High level of manual curation

DIANA TOOLS

Is a tool for determining miRNA and lncRNA interaction based on experimental studies and computational prediction

http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex

PA

(+) Prediction of Interactions

(−) Limited number of stored information on interactions

GeneCards

Provides comprehensive information about coding and non coding genes

https://www.genecards.org/

PA

(−) No Analytic Capabilities

SomamiR

Includes information about somatic mutations in miRNA or miRNA-target site sequences and on biological pathways affected by these alterations

http://compbio.uthsc.edu/SomamiR/

PA

(+) Somatic Information

PROGmiR

Give information about the potential role of miRNAs as cancer biomarker

https://omictools.com/progmir-tool

PA

(+) Highly Tailored for cancer

(−) No information for other diseases

miRCancer

Contain data about miRNA-cancer association obtained through data mining

http://mircancer.ecu.edu

PA

(+) Highly Tailored for cancer

(−) No information for other diseases

miRBase

Includes published miRNA sequence and annotation, available for download

http://www.mirbase.org/index.shtml

PA

(+) Highly Tailored for cancer

(−) No information for other diseases

miRwalk

Provides information about miRNA-target interaction

http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/

PA

(+) High potential for custom analysis

miRDB

microRNA target prediction tools

http://mirdb.org/

PA

(−) Limited Analysis

TargetScan

http://www.targetscan.org/vert_72/

PA

(+) High potential for custom analysis

miRTar.human

http://mirtar.mbc.nctu.edu.tw/human/

PA

(+) Possibility of downloading and use in local for batch analysis

miRmap

https://mirmap.ezlab.org/

PA

(+) High potential for custom analysis

miRDeep2

microRNA deep sequencing tools

http://ibis.tau.ac.il/miRNAkey/

PA

(−) Not user friendy

(−) Requires programming skills

(−) No recent updates

miRNAkey

https://bio.tools/mirnakey

PA

(−) Not user friendy

(−) Requires programming skills

- No recent updates