ESTAP statistics

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Citations per year

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

This map represents all the scientific publications referring to ESTAP per scientific context
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Protocols

ESTAP specifications

Information


Unique identifier OMICS_15131
Name ESTAP
Alternative name EST Analysis Pipeline
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Java, Shell (Bash)
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Chunhong Mao

Information


Unique identifier OMICS_15131
Name ESTAP
Alternative name EST Analysis Pipeline
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Java, Shell (Bash)
Computer skills Medium
Version 3.1.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Chunhong Mao

Publication for EST Analysis Pipeline

ESTAP citations

 (26)
library_books

EST Pipeline System: Detailed and Automated EST Data Processing and Mining

2016
PMCID: 5172240
PMID: 15629036
DOI: 10.1016/S1672-0229(03)01029-5

[…] hat most biologists would encounter when facing these tools: how to use them? Recently, some research groups have published their automated or semi-automated procedures for EST data analysis, such as ESTAP , and some other web-based systems . However, the graphical view, the well organized and connected list views, the output capability, and the job logging systems make our EST Pipeline System mor […]

library_books

Protein NMR Structures Refined without NOE Data

2014
PLoS One
PMCID: 4184813
PMID: 25279564
DOI: 10.1371/journal.pone.0108888

[…] e the target energy (Etotal; ), which consists of the default CHARMM energy with EEF1.1 solvation energy (all hydrogen effective energy functions included in the CHARMM parameters) (ECHARMM), STAP (ESTAP), and flat-bottom distance potential (Eflat). The Eflat was scaled by a factor of 10.0.(3) The refinement protocol that was used is as follows: (i) the system is minimized and heated from 100 to […]

library_books

Probing the applicability of autotransporter based surface display with the EstA autotransporter of Pseudomonas stutzeri A15

2012
Microb Cell Fact
PMCID: 3546941
PMID: 23237539
DOI: 10.1186/1475-2859-11-158

[…] EstAβL is identical to the 5′ UTR of pHERD26T-estA, which expresses the EstA AT, and was therefore expected to have similar expression levels as the latter. As a preliminary test, the P. stutzeri A15 EstAP passenger domain (from residue P27 to S325, EstAP on Figure ) was cloned as the passenger domain in the expression modules yielding pEstAβestAP and pEstAβL-estAP. The EstAP fusion protein expres […]

library_books

Meta analytical biomarker search of EST expression data reveals three differentially expressed candidates

2012
BMC Genomics
PMCID: 3521215
PMID: 23282184
DOI: 10.1186/1471-2164-13-S7-S12

[…] TW and LC selected and filtered EST libraries as well as STRING analysis. TW conceived the deployment of the statistical method and implemented and ran the EST analysis pipeline. Microarray slides were selected by LC and analyzed by TW. TW, LC, TC were involved with literature search. LC selects the genes for expression validation and STRING analysis. JW […]

library_books

Identification of tissue specific, abiotic stress responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large scale EST data sets

2011
BMC Plant Biol
PMCID: 3224124
PMID: 21592389
DOI: 10.1186/1471-2229-11-86

[…] ctively. Oligo-dT primer (T22M) was used for 3' sequencing reads of cDNA clones containing poly-A tails.Raw single-pass sequence data were retrieved from a Geospiza Finch server and downloaded to the EST Analysis Pipeline (ESTAP) [] for cleansing and analysis. Following removal of vector and low quality sequences, all sequences ≤ 50 bp in length were discarded. Remaining sequences were clustered u […]

library_books

Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes

2010
BMC Plant Biol
PMCID: 2890016
PMID: 20500869
DOI: 10.1186/1471-2229-10-96

[…] RET cultured the algae, carried out the wet bench work, built the EST analysis pipeline and drafted the manuscript. CFD participated in the design and coordination of the study and helped to draft and edit the manuscript. Both authors read and approved the final man […]


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ESTAP institution(s)
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Department of Biochemistry, University of Nevada, Reno, NV, USA; Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA; School of Computational Sciences, George Mason University, Manassas, VA, USA
ESTAP funding source(s)
This work is supported by the Samuel Roberts Noble Foundation in Ardmore Oklahoma, the University of Nevada at Reno and the Virginia Bioinformatics Institute.

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