Annocript protocols

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Annocript specifications

Information


Unique identifier OMICS_07588
Name Annocript
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A transcriptome
Input format FASTA
Operating system Unix/Linux
Database management system MySQL
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.2
Stability Stable
Requirements
MySQL database server, Perl, BioPerl, Python, R, Blast+, Portrait, dna2pep
Maintained Yes

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Documentation


Maintainer


  • person_outline Remo Sanges <>

Publication for Annocript

Annocript in pipelines

 (3)
2018
PMCID: 5955879
PMID: 29599523
DOI: 10.1038/s41396-018-0094-0

[…] 7 real-time pcr system (life technologies)., the raw reads (accession e-mtab-6076) were adapter filtered and quality trimmed using trimmomatic [] then assembled using trinity [] and annotated using annocript pipeline [] (supplementary file ). the expression levels were quantified using bowtie []. transcripts <200 nucleotides or with an expression <1 count per million (cpm) were removed., […]

2017
PMCID: 5241685
PMID: 28098242
DOI: 10.1038/srep40817

[…] from rockhopper and the absolute value of |log2 fold change| ≥ 1 as the threshold to judge significant differences in gene expression., to annotate the hypothetical degs, we used the custom pipeline annocript (https://github.com/frankmusacchia/annocript/tree/master/guide). we used swiss-prot (sp) and uniref90 (version: august 2015) databases for blastp searches with the following parameters: […]

2017
PMCID: 5476593
PMID: 28630429
DOI: 10.1038/s41598-017-03741-6

[…] reads against the assembled transcriptome using bowtie (ver. 1.1). to count the reads mapped we used samtools (ver. 0.1.19-44428 cd). the resulting reference transcriptome was annotated using annocript software that aligns transcripts against known proteins, domains and non-coding rnas (supplementary information). in order to refine domain annotation we used meta-clade (ugarte et al., […]


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Annocript in publications

 (10)
PMCID: 5846289
PMID: 29564081
DOI: 10.1093/aobpla/ply013

[…] a heat stress and control transcriptome for b. depauperata was therefore constructed from independent heat stress and control rna-seq libraries and assembled using trinity () and was annotated using annocript (). since b. depauperata is a polyploid, we disentangled the homologs using homeosplitter (). when we used the b. depauperata transcriptome as reference, ~100185 junctions were identified. […]

PMCID: 5637092
PMID: 29020917
DOI: 10.1186/s12864-017-4144-1

[…] ncbi’s genbank and from swissprot. to identify gene categories and pfam terms enriched in the pairwise comparisons between the four tissues a go/pfam term enrichment analysis was performed using the annocript software [] and the fisher exact test (adjusted p-value <0.01) in r package []. clean reads were mapped back onto the assembled transcriptome using rsem software and read count […]

PMCID: 5584759
PMID: 28873438
DOI: 10.1371/journal.pone.0184090

[…] which we will refer to as ‘transcripts’ for the sake of discussion. the completeness of the transcriptome was assessed by use of the software cegma []., to annotate the transcripts, we used the annocript pipeline [] which runs different blast programs to align sequences against the uniprot database: i) blastp against the uniref90 and swissprot databases (parameters: word_size = 4 evalue = […]

PMCID: 5501815
PMID: 28687784
DOI: 10.1038/s41598-017-05377-y

[…] in species and collection time (supplementary table )., for all mapped reads, we performed “de novo” transcriptome assembly, which resulted in retrieval of 214,688 transcripts. we used the annocript pipeline and integrated the reference information to annotate these transcripts, resulting in annotation of 119,017 kiwifruit protein-coding transcripts which originated from 39,040 loci […]

PMCID: 5417585
PMID: 28472112
DOI: 10.1371/journal.pone.0176956

[…] sequences were present as single-copy or duplicated transcripts in the assembly, suggesting that it is mostly complete. for annotation and gene ontology assignments we passed the assembly through annocript, blasting against the uniref90, swissprot and conserved domain databases with an e-value cut-off value of 1e-5 [, ]. we used these annotations for all subsequent analysis., we quantified […]


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Annocript institution(s)
Laboratory of Animal Physiology and Evolution, Napoli, Italy

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