annot8r protocols

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annot8r specifications

Information


Unique identifier OMICS_07589
Name annot8r
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1.1
Stability Stable
Requirements
BioPerl, CPAN, PostgreSQL, BLAST
Maintained Yes

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Publication for annot8r

annot8r in pipelines

 (6)
2017
PMCID: 5466607
PMID: 28600526
DOI: 10.1038/s41598-017-03431-3

[…] to gupta et al.. then, all the unigenes of 1627 were annotated using a blastx search of the uniprot database (http://www.ebi.ac.uk/uniprot/). go-kegg-ec annotation was performed based on the annot8r platform, . tdfs were also checked for putative function against the arabidopsis database and the cotton genome database (institute of cotton research of caas) using the fasta tool […]

2013
PMCID: 3630068
PMID: 23394720
DOI: 10.1186/1471-2164-14-87

[…] edited sequence for each affected contig. annotations with gene ontology (go), enzyme commission (ec) and kyoto encyclopedia of genes and genomes (kegg) terms were inferred for these proteins using annot8r (version 1.1.1) [], using the annotated sequences available in uniref100 []. up to 10 annotations based on a blast similarity bitscore cut-off of 55 were obtained for each annotation set. […]

2010
PMCID: 2867827
PMID: 20374642
DOI: 10.1186/1471-2164-11-227

[…] the resulting contigs and singletons were compared to a set of databases maintained locally (listed in supplementary table 1) using tblastx and blastx. functional categories were analyzed using annot8r []. signal sequence prediction was performed using signalp3.0 program []. prediction of trans-membrane domains were conducted using tmhmm software []. blast results comparisons were performed […]

2010
PMCID: 2995126
PMID: 20971988
DOI: 10.1093/bioinformatics/btq599

[…] schemas; and (iv) providing other, generic, functions useful for bioinformatic module development., we also built two example applications. first, a software server with the blast, interproscan, annot8r and ssaha2 software deployed by default; additional plugins can be generated by the community. second, a web-based database for storing experimental information from rnai experiments. we used […]

2010
PMCID: 2995126
PMID: 20971988
DOI: 10.1093/bioinformatics/btq599

[…] library. further, an external jquery-utilizing library, dynatree (http://code.google.com/p/dynatree), is used to produce ‘check-box trees’. commonly used annotation software, such as blast, annot8r, interproscan and ssaha2 (; ; ; ), were integrated into biosoftwarebench, but using them requires that they are installed on the server (not all software needs to be installed: administrators […]


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annot8r in publications

 (39)
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] transcriptome sequence displayed an overall good agreement (82.5%) with the coding sequences reported for the reference genome., the correctly assembled sequences were functionally annotated using annot8r program. all the assembled sequences were compared against uniprot database with an e-value 10−1. the various functional categories named as go (gene ontology), ec (enzyme classification) […]

PMCID: 5759876
PMID: 29310579
DOI: 10.1186/s12864-017-4388-9

[…] were predicted and annotated based on similarity to the carbohydrate-active enzymes (cazy) (http://www.cazy.org/) database, enzyme commission number (ec) database (http://enzyme.expasy.org) using annot8r pipeline (http://www.nematodes.org/bioinformatics/annot8r) and pfam alignments., an all-versus-all blastp alignment [] (50% identity; e-value 1e-4 cut-off) was performed on the extracted […]

PMCID: 5440251
PMID: 28560168
DOI: 10.1016/j.gdata.2017.05.009

[…] coverage of 13 × and a total size of 33.4 mb. using in-house rna-seq and proteomic data as additional evidence, 9820 gene models were predicted using maker and were functionally annotated with annot8r ., image 2 , the genome of r. toruloides strain cgmcc 2.1609 assembles as 33.4 mb, which is larger than the ~ 20.3 mb sequenced genomes of haploid r. toruloides strains , , , . […]

PMCID: 5112563
PMID: 27853259
DOI: 10.1038/srep37244

[…] molecular function (f) & cellular component (c)], enzyme classification (ec) and kyoto encyclopedia of genes and genomes (kegg) were based on highest scoring hits attained for the sequences using annot8r tool. annotation of tea unigenes against go database was resulted in significant hits for 16,778 transcripts in ‘h’ (p = 16,249, f = 15,253, c = 16,066), 17,270 transcripts in ‘t’ (p = 16,777, […]

PMCID: 4964330
PMID: 27465480
DOI: 10.1038/srep30412

[…] most of the defense related genes were expressed in s4_rg., gene ontology (go) categories of up-regulated transcripts within each stage of disease progression in rg and sg were identified using annot8r. biological processes and metabolic pathways go enrichment analysis revealed that go terms, namely response to stimulus were found to be highly enriched in s1_rg, where in response […]


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annot8r institution(s)
Department of Biochemistry, University of Leicester, Lancaster Road, Leicester, UK

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