CSTminer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CSTminer

Tool usage distribution map

This map represents all the scientific publications referring to CSTminer per scientific context
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Associated diseases


Popular tool citations

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CSTminer specifications


Unique identifier OMICS_24028
Name CSTminer
Interface Web user interface
Restrictions to use None
Input data A graphical output of the detected CSTs.
Computer skills Basic
Maintained Yes


  • person_outline Graziano Pesole

Publication for CSTminer

CSTminer citations


Molecular Functions of Long Non Coding RNAs in Plants

PMCID: 3899965
PMID: 24704849
DOI: 10.3390/genes3010176

[…] hmm [], GenScan [], ESTScan2 [], ANGLE [] and ORF-Predictor []. More sophisticated bioinformatics tools for estimating the protein-coding potential of a RNA sequence include CRITICA [], DIANA-EST [], CSTminer [], CONC [], Coding Potential Calculator [], integrated ncRNA finder [] and RNAcode []. The in silico approach has been successfully applied to identifying lncRNAs in both plants [] and anima […]


Accurate discrimination of conserved coding and non coding regions through multiple indicators of evolutionary dynamics

BMC Bioinformatics
PMCID: 2758873
PMID: 19737408
DOI: 10.1186/1471-2105-10-282

[…] CSTminer [,] is an application previously developed by our group to identify CSTs and classify them as coding or non-coding based on their evolutionary dynamics. It relies on a single scoring function […]


Differentiating Protein Coding and Noncoding RNA: Challenges and Ambiguities

PLoS Comput Biol
PMCID: 2518207
PMID: 19043537
DOI: 10.1371/journal.pcbi.1000176

[…] Pfam , and SUPERFAMILY .A few methods designed to detect ORF conservation can be used to distinguish ncRNAs from mRNAs on a transcriptome-wide scale. These comparative approaches include the programs CSTminer , and CRITICA , both of which exploit the tendency for protein-coding sequences to favor synonymous base changes (i.e., changes that do not result in amino acid substitution) over non-synonym […]


Genome wide identification of coding and non coding conserved sequence tags in human and mouse genomes

BMC Genomics
PMCID: 2442843
PMID: 18547402
DOI: 10.1186/1471-2164-9-277

[…] We empirically determined that for large scale comparisons CSTminer gives optimal results with sequences of 100 Kbp with 1 Kbp overlap. Indeed this value allows a good balance between computational speed and the occurrence of CST fragmentation at the border o […]


Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus

BMC Genomics
PMCID: 1636649
PMID: 17092333
DOI: 10.1186/1471-2164-7-288

[…] re not further analysed. Assessment of the coding nature of detected CSTs was done through the computation of a coding potential score (CPS) on the total CST and on CST sliding windows and, using the CSTminer program [,]. CPS values higher than 7.71 indicate a coding potential of the related CST, and CPS values lower than 6.74 indicate noncoding CSTs, with an estimated false positive rate < 1% []. […]


EGASP: the human ENCODE Genome Annotation Assessment Project

Genome Biol
PMCID: 1810551
PMID: 16925836
DOI: 10.1186/gb-2006-7-s1-s2

[…] d Steitz [] for an in-depth review on U12 splicing).Six programs submitted predictions that were included in category 6 (exon only predictions). ASPIC predicted only introns for the training regions, CSTMINER predicted coding regions, but did not provide strand information or splice site boundaries, DOGFISH-C-E and UNCOVER predicted only novel exons, and AUGUSTUS-exon and SPIDA predicted exons but […]

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CSTminer institution(s)
Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita e Ricerca, CASPUR, Rome, Italy; Istituto Tecnologie Biomediche, Sezione di Bioinformatica e Genomica, Consiglio Nazionale delle Ricerche, Bari, Italy; University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie, Milan, Italy
CSTminer funding source(s)
Supported by FIRB project Bioinformatica per la Genomica e la Proteomica, Cluster C03 ‘Studio di geni di interesse biomedico e agroalimentare’ (Ministero dell’Istruzione e Ricerca Scientifica, Italy) and by Telethon.

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