ESTScan protocols

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ESTScan specifications

Information


Unique identifier OMICS_08423
Name ESTScan
Alternative names ESTSCAN, ESTSCAN2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Documentation


Information


Unique identifier OMICS_08423
Name ESTScan
Alternative names ESTSCAN, ESTSCAN2
Interface Web user interface
Restrictions to use None
Programming languages C
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Documentation


Publications for ESTScan

ESTScan in pipelines

 (93)
2018
PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] databases. homology searches against the nr database were performed by blastx with a cut-off e-value of 1e-5. unigenes having no homologs in the nr and swissprot databases were scanned using estscan []., gene expression levels were estimated by rsem []. for each sample, two biological replicates were sequenced and the correlation coefficients (r2) between replicates were calculated using […]

2018
PMCID: 5809607
PMID: 29434336
DOI: 10.1038/s41598-018-21268-2

[…] groups) databases. the results from these alignments were used to determine the direction of these sequences. lastly, the sequences that were not aligned to any database were subjected to a estscan analysis. for function annotation, a local blast was used to search against the nt (ncbi nucleotide database), nr, swiss-prot, kegg and cog databases. blast hits from the nr database […]

2018
PMCID: 5859003
PMID: 29556854
DOI: 10.1186/s13568-018-0567-6

[…] of unigenes (5′-3′ direction) were defined by the highest rank in the blast results. in addition, the cds of some unigenes, that could not be aligned to the above databases, were predicted by estscan software. in total, 16,578 unigenes were identified to harbor their cds, where the cds of 11,975 unigenes were identified by blast alignment and that of 4603 were estimated by the estscan., […]

2018
PMCID: 5859003
PMID: 29556854
DOI: 10.1186/s13568-018-0567-6

[…] results were used to annotate unigenes and decide the sequence direction of each unigene. additionally, some unigenes that had no alignment hit in the above databases were further estimated by using estscan (3.0.3) software (iseli et al. ) to predict their protein coding sequences (cds). with nr and swiss-prot annotation, blast2go software (conesa et al. ) was used to perform gene ontology (go) […]

2018
PMCID: 5944168
PMID: 29743016
DOI: 10.1186/s12864-018-4707-9

[…] databases were mutually contradictory, a priority order of nr, swiss-prot, kegg, and cog was followed to decide the annotation. nevertheless, if a unigene did not align to any of the databases, estscan software was chosen to infer the direction of transcription []., each of the 12 e. ferox seed cdna libraries was aligned separately to the transcriptome assemblies using bowtie []. […]


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ESTScan in publications

 (419)
PMCID: 5944168
PMID: 29743016
DOI: 10.1186/s12864-018-4707-9

[…] databases were mutually contradictory, a priority order of nr, swiss-prot, kegg, and cog was followed to decide the annotation. nevertheless, if a unigene did not align to any of the databases, estscan software was chosen to infer the direction of transcription []., each of the 12 e. ferox seed cdna libraries was aligned separately to the transcriptome assemblies using bowtie []. […]

PMCID: 5867891
PMID: 29558449
DOI: 10.3390/genes9030170

[…] []. sequences matching with proteins were excluded from further analysis. the remaining sequences had their coding potential evaluated using transdecoder (version 2.0) [], cpc (version 1) [] and estscan (version 2.1) []. if a transcript was predicted as potential coding by at least one of the tools, it was considered as a potential protein coding or pseudogene and excluded from the final […]

PMCID: 5827294
PMID: 29520289
DOI: 10.3389/fpls.2018.00217

[…] standard codons. thus, we acquired both the nucleotide sequences (5′−3′) and the amino acid sequences of the unigene coding region. unigenes that could not be aligned to any database were scanned by estscan, producing nucleotide sequence (5′−3′) direction and the amino acid sequence of the predicted coding region (iseli et al., )., to characterize degs response to salt stress and recovery […]

PMCID: 5809607
PMID: 29434336
DOI: 10.1038/s41598-018-21268-2

[…] groups) databases. the results from these alignments were used to determine the direction of these sequences. lastly, the sequences that were not aligned to any database were subjected to a estscan analysis. for function annotation, a local blast was used to search against the nt (ncbi nucleotide database), nr, swiss-prot, kegg and cog databases. blast hits from the nr database […]

PMCID: 5800542
PMID: 29408859
DOI: 10.1371/journal.pone.0191213

[…] lengths of the peptides blasted against the nr, swiss-prot and kegg databases were mainly distributed in the range of approximately 80 to 1,000 amino acid residues, whereas the peptides predicted by estscan were mainly distributed in the range of approximately 40 to 600 amino acid residues ()., note: q20 represents an error rate less than 0.01, and q30 represents an error rate less than 0.001. […]


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ESTScan institution(s)
Swiss Institute of Bioinformatics, Switzerland

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