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Number of citations per year for the bioinformatics software tool annot8r
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Tool usage distribution map

This map represents all the scientific publications referring to annot8r per scientific context
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Protocols

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

Versioning


No version available

Publication for annot8r

annot8r citations

 (45)
library_books

Transcriptome and Co Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

2018
Sci Rep
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] hreshold of 10−5. The transcripts that had no sequence similarity but may belong to different regions of similar gene were identified and clustered using Dissimilar Sequence (DS) clustering approach. Annot8r program was used to annotate the correctly assembled transcripts with an E-value threshold of 10−1 (http://www.nematodes.org/bioinformatics/annot8r). To derive transcription factor family rela […]

library_books

Gene trait matching across the Bifidobacterium longum pan genome reveals considerable diversity in carbohydrate catabolism among human infant strains

2018
BMC Genomics
PMCID: 5759876
PMID: 29310579
DOI: 10.1186/s12864-017-4388-9

[…] ses 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. […]

call_split

Differential transcript profiling alters regulatory gene expression during the development of Gossypium arboreum, G.stocksii and somatic hybrids

2017
Sci Rep
PMCID: 5466607
PMID: 28600526
DOI: 10.1038/s41598-017-03431-3
call_split See protocol

[…] ccording 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 (http://www […]

library_books

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609

2017
Genom Data
PMCID: 5440251
PMID: 28560168
DOI: 10.1016/j.gdata.2017.05.009

[…] verage 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 . 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 , , , . Of the assembled CGMCC 2. […]

library_books

Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA seq Technology

2016
Sci Rep
PMCID: 5112563
PMID: 27853259
DOI: 10.1038/srep37244

[…] Annotations for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Enzyme Commission Codes (EC) for assembled transcripts were carried out using Annot8r annotation tool against UniProt database. Based on highest bit score and E-value, top-hits were selected. For expression measurement as FPKM (Fragments per kilobase of transcript per million m […]

library_books

Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)

2016
Sci Rep
PMCID: 4964330
PMID: 27465480
DOI: 10.1038/srep30412

[…] //www.kegg.jp/kegg/download/) and EC entries. The best hit among the multiple hits for the query transcript sequence was selected on the basis of highest bitscore and E-value (1e–5). Annotation tool, annot8r was used for GO, EC and KEGG based annotations and statistics. Classification and identification of various transcription factors were performed against the Plant transcription factor database […]


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

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