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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

 (5)
library_books

Molecular Functions of Long Non Coding RNAs in Plants

2012
PMCID: 3899965
PMID: 24704849
DOI: 10.3390/genes3010176

[…] [], 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 [] […]

library_books

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

2009
PMCID: 2758873
PMID: 19737408
DOI: 10.1186/1471-2105-10-282

[…] used - suggesting that, using the features developed here, a relatively small number of instances can adequately represent the diversity of evolutionary dynamics of coding and non-coding csts., 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 […]

library_books

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

2008
PMCID: 2442843
PMID: 18547402
DOI: 10.1186/1471-2164-9-277

[…] classification heavily dependent on the quality of the annotation of the genomes under analysis and it is obviously less applicable to new – poorly annotated – genomes., we previously developed cstminer, a tool that does not suffer from these limitations as it identifies conserved sequences (conserved sequence tags – csts) and classifies them as coding or non-coding by evaluating […]

library_books

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

2006
PMCID: 1636649
PMID: 17092333
DOI: 10.1186/1471-2164-7-288

[…] 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

Distinguishing Protein Coding from Non Coding RNAs through Support Vector Machines

2006
PMCID: 1449884
PMID: 16683024
DOI: 10.1371/journal.pgen.0020029

[…] within cdnas, expressed sequence tags [ests], or prokaryotic genomic dnas) have been applied to this task. the analysis of dna alignments and codon usage is one of the most widely used strategies. cstminer [] identifies conserved sequence tags by comparing cross-species dna alignments, based on the observation that in homologous regions, synonymous changes (i.e., base changes without amino […]


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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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