AutoFACT pipeline

AutoFACT specifications

Information


Unique identifier OMICS_07591
Name AutoFACT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 3.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline AutoFACT <>

Publication for AutoFACT

AutoFACT IN pipelines

 (4)
2013
PMCID: 3534657
PMID: 23301019
DOI: 10.1371/journal.pone.0053047

[…] [18]. transfer rna (trna) genes were located with trnascan-se [19]. protein-coding genes were identified by the glimmer gene finder [20]. whole-genome annotation and analysis were performed with the autofact annotation tool [21]. clusters of regularly interspaced repeats (crispr) were identified by crispr finder [22]. signal peptides were predicted with signalp v. 3.0 [23]. the annotated genome […]

2013
PMCID: 3608089
PMID: 23497193
DOI: 10.1186/1471-2164-14-153

[…] inference of gene expression by reads per kilobase of exon per million mapped reads (rpkm) was assigned, making it possible to infer the expression level of genes in the subtractive library [63]., autofact software [64] was used for automatic annotation of the sequences, through several blastx searches (e-value cutoff of 1e-5) against protein databases including nr (non-redundant from ncbi), […]

2013
PMCID: 3859324
PMID: 23857904
DOI: 10.1093/dnares/dst031

[…] amazonensis reads generated by illumina., n/a, not available., the final set of gene models were annotated automatically by comparing them against protein databases (blastp) and summarizing with autofact software. the results indicated that 55% of the gene models showed high sequence similarity (e-value 1 × 10−10) to functionally annotated proteins, whereas 42% of the models were similar […]

2010
PMCID: 2864506
PMID: 20454581
DOI: 10.1155/2010/246738

[…] of cocoon from microbial infection (table 1 and supplementary information)., out of the 648 clusters, 353 showed a hit to the protein database uniref90 as determined by blastx results using autofact. in order to functionally categorize these clusters, uniprot id of each of these sequences was searched against quickgo (http://www.ebi.ac.uk/ego/), the web based browser of the gene […]

AutoFACT institution(s)
Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada

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