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FASTAptamer specifications

Information


Unique identifier OMICS_10074
Name FASTAptamer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.9
Stability Stable
Maintained Yes

Subtool


  • Galaxy ToolShed

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galaxy.png

Versioning


No version available

Maintainer


  • person_outline Donald H. Burke <>

Information


Unique identifier OMICS_10074
Name FASTAptamer
Interface Web user interface
Restrictions to use None
Programming languages Perl
Computer skills Basic
Version 1.0.9
Stability Stable
Maintained Yes

Subtool


  • Galaxy ToolShed

Maintainer


  • person_outline Donald H. Burke <>

Publication for FASTAptamer

FASTAptamer citations

 (27)
library_books

Notos a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types

2018
PMCID: 5870242
PMID: 29587630
DOI: 10.1186/s12859-018-2115-4

[…] return grant to i. bulla (bu 2685/4-1)., all data generated or analyzed during this study are included in this published article and its supplementary information files. notos is available in the galaxy toolshed and can also be downloaded from http://ihpe.univ-perp.fr/acces-aux-donnees/., the authors are grateful to rémi emans for technical support, and david duval and céline cosseau […]

library_books

Uncovering the molecular mechanisms of lignocellulose digestion in shipworms

2018
PMCID: 5840672
PMID: 29527236
DOI: 10.1186/s13068-018-1058-3

[…] were mapped onto the transcriptomes of the three molluscs and normalized expression values (tpm = transcripts per kilobase million) were calculated for each transcript using salmon (part of the galaxy toolshed) []. although all three animals provided raw reads with high quality and could be used to assemble a reference transcriptome, tpm values from one animal were found to be poorly […]

library_books

An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion

2018
PMCID: 5823890
PMID: 29472725
DOI: 10.1038/s41467-018-03142-x

[…] from ncbi (accession: srr921648) and mapped onto the published transcriptome of thermobia to determine normalized expression values (tpm = transcripts per kilobase million) using salmon (part of the galaxy toolshed)., the native sequences coding for tdaa15a and tdaa15b were cloned using cdna generated from rna extracted from thermobia. briefly, total rna was extracted from one animal using […]

library_books

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework

2018
PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. these resources are documented on github and freely available through the galaxy toolshed, as well as a publicly accessible metaproteomics gateway galaxy instance. these documented workflows are well suited for the training of novice metaproteomics researchers, […]

library_books

Aptamer Bioinformatics

2017
PMCID: 5751119
PMID: 29186809
DOI: 10.3390/ijms18122516

[…] for motif-based clustering as the platform was designed for general genomic projects. , an easy-to-use, aptamer-specific bioinformatics tool to address the clustering based on primary sequence is fastaptamer []. fastaptamer consists of a library of modular perl scripts and is compatible across unix-like systems (or a windows system with a perl interpreter installed). count, compare, cluster, […]

library_books

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

2017
PMCID: 5691353
PMID: 29048555
DOI: 10.1093/gigascience/gix099

[…] network that already included an ng-sequencer and that manages the main steps of standard and reproducible data processing until the final analysis, making the results available inside galaxy., the galaxy toolshed provides an efficient way to share tools. however, it may be difficult to maintain and be able to run different versions of a same tool, especially if the various versions make use […]


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FASTAptamer institution(s)
Department of Biochemistry, University of Missouri, Columbia, MO, USA
FASTAptamer funding source(s)
Funding for this work was provided by NSF [CHE-1057506] (Chemistry of Life Processes) & NASA [NAG5-12360] (NASA Exobiology Program)

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