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Citations per year

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

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

Manatee specifications

Information


Unique identifier OMICS_30563
Name Manatee
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
Database management system MySQL
Computer skills Advanced
Stability Stable
Maintained Yes

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Manatee citations

 (38)
library_books

Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny

2017
Front Physiol
PMCID: 5611445
PMID: 28979209
DOI: 10.3389/fphys.2017.00670

[…] renian DNA reads were sequenced on Illumina GAIIx and HiSeq2500 (Illumina Inc.; San Diego, California, USA) platforms. Sequenced reads were assembled to reference sequences of the white rhinoceros or manatee (Trichechus manatus) using the “map to reference” feature in Geneious R9.1 (Biomatters Ltd.; Auckland, New Zealand) at 20% maximum mismatch per read and consensus sequences were generated.For […]

call_split

Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane Degrading Bacterium

2017
Genome Announc
PMCID: 5597755
PMID: 28912314
DOI: 10.1128/genomeA.00897-17
call_split See protocol

[…] tation pipeline was used for coding gene prediction and functional annotation (). The output annotations were loaded into a MySQL Chado relational database and accessed through the visualization tool Manatee (http://manatee.sourceforge.net). Protein-coding genes were predicted using Glimmer version 3 (), and noncoding RNA genes were predicted using tRNAscan-SE () and RNAmmer version 1.2 ().The com […]

library_books

Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases

2017
Front Microbiol
PMCID: 5318389
PMID: 28270800
DOI: 10.3389/fmicb.2017.00243

[…] usly described (; ) after sequencing at the Genoscope (Evry, France) or at the Center for Genome Research (Liverpool, UK). After a preliminary automatic structural and functional annotation using the Manatee pipeline, orthologous coding sequences were clustered using orthoMCL, then included into the Cyanorak v2 information system to manually refine the annotation of genes potentially involved in p […]

library_books

Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat

2017
PMCID: 5374385
PMID: 28230808
DOI: 10.3390/microorganisms5010008

[…] e identification with Glimmer, Hidden Markov Model (HMM) searches, transmembrane (Tm) HMM searches, SignalP predictions, and automatic annotations from AutoAnnotate. Additionally, the annotation tool Manatee [] was used to manually review and confirm the annotation of every gene. Pseudogenes contained one or more mutations that would ablate expression; each inactivating mutation was subsequently c […]

library_books

Draft Genome Sequence of Cloacibacterium normanense NRS 1 Isolated from Municipal Wastewater

2016
Genome Announc
PMCID: 5159580
PMID: 27979947
DOI: 10.1128/genomeA.01397-16

[…] 666 bp and an N50 value of 112,075 bp ().The IGS Annotation Engine was used for structural and functional annotation of the sequences (http://ae.igs.umaryland.edu/cgi/index.cgi, reference: 21677861). Manatee was used to view annotations (http://manatee.sourceforge.net). Manatee identified 38 tRNAs, three rRNAs, and 2,579 open reading frames, 88.5% of which are coding regions. The Comprehensive Ant […]

library_books

Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long Term at Elevated Copper Levels

2016
Genome Announc
PMCID: 5122684
PMID: 27881542
DOI: 10.1128/genomeA.01311-16

[…] ly was conducted using SPAdes version 3.6 (). The IGS Annotation Engine was used for structural and functional annotation of the four draft genomes (http://ae.igs.umaryland.edu/cgi/index.cgi) (). The Manatee tool was used for viewing the data (http://manatee.sourceforge.net). A. macleodii strain ATCC 27126 (accession no. CP003841.1), representative of the shallow-water ecotype, served as the refer […]


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