ESTScan pipeline

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 citations

 (8)
2018
PMCID: 5859003

[…] 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. 1999) to predict their protein coding sequences (cds). with nr and swiss-prot annotation, blast2go software (conesa et al. 2005) was used to perform gene […]

2017
PMCID: 5747154

[…] libraries, the order of the sequence of unigene is determined according to the priority of nr, swiss-prot, kegg and cog. unigene is not comparable to the above four libraries. we used the software estscan to determine the sequence direction., expression levels of mirnas were determined based on sequence analysis of mature mirnas that share the same sequence and expression levels. […]

2016
PMCID: 4804210

[…] 57,760 unigenes, 46,485 contained coding sequences as determined by searching unigene sequences against protein databases using blastx (e-value <0.00001) or by predicting with estscan 3.0 (http://estscan.sourceforge.net/) (table 1)., to facilitate the global analysis of the bark transcriptome, all predicted unigenes were assigned to different functional categories with blast2go. […]

2015
PMCID: 4561955

[…] annotation of the unigenes. in case of conflicting results among the databases, the priority order was defined as nr, swiss-prot, kegg and cog. if the unigenes could not be aligned to all databases, estscan v3.0.239 was used to decide sequence annotation. the read-mapping was processed by burrows-wheeler aligner using the transcriptome of progenies as references40., the fpkm method41 was used […]

2014
PMCID: 3914838

[…] no less than 100 bp, using blastx and estscan (figure 1). 21 063 unigenes with homologous matches in the four protein databases were identified to be cds. other unigenes were processed with estscan and a total of 1 805 unigenes were detected. the unigenes without identified coding regions were likely to be too short to meet the criteria for cds prediction, or may be non-coding rnas. […]

ESTScan institution(s)
Swiss Institute of Bioinformatics, Switzerland

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