CSTminer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CSTminer
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Tool usage distribution map

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

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Popular tool citations

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CSTminer specifications

Information


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

Maintainer


  • person_outline Graziano Pesole

Publication for CSTminer

CSTminer citations

 (7)
library_books

Molecular Functions of Long Non Coding RNAs in Plants

2012
Genes
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 […]

library_books

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

2009
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 […]

library_books

Differentiating Protein Coding and Noncoding RNA: Challenges and Ambiguities

2008
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 […]

library_books

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

2008
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 […]

library_books

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

2006
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% []. […]

library_books

EGASP: the human ENCODE Genome Annotation Assessment Project

2006
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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