AutoFACT protocols

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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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  • person_outline AutoFACT <>

Publication for AutoFACT

AutoFACT in pipelines

 (12)
2018
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] []. sequence domains were assigned by rps-blast (v2.2.26) against pfam (oct 31, 2012), smart (oct 31, 2012) and cdd (oct 31, 2012). the blast protein and domain searches were then summarised using autofact version 3.4 []. gene ontology (go) functional assignment was conducted using david [] to level 1 and tests for enrichment were performed based on an ease score threshold 0.1, […]

2016
PMCID: 5053433
PMID: 27711117
DOI: 10.1371/journal.pone.0163379

[…] overlap with any other read were classified as “singletons”. three different annotation programs were used to annotate the pool of merged contigs renamed as unigenes, fullengthernext, sma3s [] and autofact []. these annotators were used to annotate predicted genes using default parameters. go terms were retrieved from the annotation process and used for the de novo functional annotation […]

2015
PMCID: 4673725
PMID: 26664701
DOI: 10.1186/s40793-015-0116-8

[…] was conducted using glimmer 3 [] in rast server [] with automatic fixation of errors and frame shifts. functional assignment of the predicted protein coding sequences (cdss) was performed using autofact [] with the results of blastp or rps-blast with uniref100, nr, cog, and pfam databases. for the accurate annotation, the functional assignment results from the rast server and blast […]

2014
PMCID: 4248463
PMID: 25407319
DOI: 10.1186/s12870-014-0301-8

[…] especially in cases such as the present analysis, where the sequences come from different species), discard sequences with ambiguities (ns) and return only reads with unique alignments., the autofact program [] was used to perform an automatic annotation of all e. grandis transcripts. the main feature of autofact is its ability to perform gene annotation based on sequence similarity […]

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

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


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AutoFACT in publications

 (45)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] []. sequence domains were assigned by rps-blast (v2.2.26) against pfam (oct 31, 2012), smart (oct 31, 2012) and cdd (oct 31, 2012). the blast protein and domain searches were then summarised using autofact version 3.4 []. gene ontology (go) functional assignment was conducted using david [] to level 1 and tests for enrichment were performed based on an ease score threshold 0.1, […]

PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] in the ceratocystis genus and in the closely related species huntiella moniliformis might be directly associated to the lower gene content.fig. 1, gene models of c. cacaofunesta were annotated using autofact []. from the 7382 queries set, 6609 (89.5%) genes showed significant matches for gene descriptions (additional file ). annotation of all the 6609 genes was performed using the gene ontology […]

PMCID: 5219037
PMID: 27766357
DOI: 10.1007/s00253-016-7928-3

[…] were established using protparam (expasy) (gasteiger et al. ), and protein binding regions have been predicted with predictprotein server (rost et al. ). the genomes were initially annotated using autofact (koski et al. ) and subsequently verified manually using kodon (applied maths, austin, tx, usa). we screened for orfs with a length ≥75 nt preceded by a visually recognizable […]

PMCID: 5053433
PMID: 27711117
DOI: 10.1371/journal.pone.0163379

[…] overlap with any other read were classified as “singletons”. three different annotation programs were used to annotate the pool of merged contigs renamed as unigenes, fullengthernext, sma3s [] and autofact []. these annotators were used to annotate predicted genes using default parameters. go terms were retrieved from the annotation process and used for the de novo functional annotation […]

PMCID: 5009977
PMID: 27587820
DOI: 10.1128/genomeA.00903-16

[…] software was used to close gaps between the contigs, and manual curation was performed to improve the gaps and to verify the assembly. automatic annotation was performed using the rast server () and autofact (). protein-coding gene sequences were predicted by glimmer version 3.0 (), and rrnas and trnas were detected in rast. the protein-coding genes were aligned to those in the kegg, cog, […]


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

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