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Sma3s specifications

Information


Unique identifier OMICS_10632
Name Sma3s
Alternative name Sequence massive annotator using 3 modules
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 2
Stability Stable
Requirements
Bioperl
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
    • Mycoplasma pneumoniae
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus laevis

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Versioning


No version available

Maintainer


  • person_outline Antonio Perez-Pulido

Publications for Sequence massive annotator using 3 modules

Sma3s citations

 (11)
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Draft Genome Sequences of the Oomycete Pilasporangium apinafurcum Strains JCM 30513 and JCM 30514, Formerly Classified as Pythium apinafurcum

2017
Genome Announc
PMCID: 5578851
PMID: 28860253
DOI: 10.1128/genomeA.00899-17
call_split See protocol

[…] ultimum var. sporangiiferum BR650 (); 13,996 (JCM 30153) and 14,069 (JCM 30514) protein-coding genes were predicted. These numbers are similar with those reported for other pythiaceous species (, ). Sma3s version 2013-09-01 () with the UniProt-TrEMBL release 2015_11 and UniProt-SwissProt release 2015_11 databases enabled functional annotation of 2,665 and 1,369 genes for JCM 30513 and 2,697 and 1 […]

library_books

The transcriptional response to the olive fruit fly (Bactrocera oleae) reveals extended differences between tolerant and susceptible olive (Olea europaea L.) varieties

2017
PLoS One
PMCID: 5552259
PMID: 28797083
DOI: 10.1371/journal.pone.0183050

[…] ith protein domain information was performed with InterProScan 5.0. A plant GO-Slim reduction was carried out to summarize the functional content of the dataset. To complete the functional annotation Sma3s was also used []. Plant taxonomic division from UniProt was selected as source of annotations, and the transcriptomic sequences were enriched with keywords, InterPro domains and motifs, and GO t […]

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De novo Analysis of the Epiphytic Transcriptome of the Cucurbit Powdery Mildew Fungus Podosphaera xanthii and Identification of Candidate Secreted Effector Proteins

2016
PLoS One
PMCID: 5053433
PMID: 27711117
DOI: 10.1371/journal.pone.0163379
call_split See protocol

[…] no significant 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 annot […]

library_books

Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae)

2016
Genome Biol Evol
PMCID: 5381614
PMID: 27694476
DOI: 10.1093/gbe/evw235

[…] The initial assignment of Gene Ontology (GO) terms for predicted proteins was performed using the UniProtKB/Swiss-Prot database () and the third module of the Sma3s program (), modified to accept only reciprocal BLAST hits for annotation. The initial annotations were merged with GO assignments provided by the InterPro database () search using the InterProSc […]

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Draft Genome Sequence of Raffaelea quercivora JCM 11526, a Japanese Oak Wilt Pathogen Associated with the Platypodid Beetle, Platypus quercivorus

2016
Genome Announc
PMCID: 4966477
PMID: 27469944
DOI: 10.1128/genomeA.00755-16
call_split See protocol

[…] peatMasker and RepeatRunner (http://www.yandell-lab.org/software/repeatrunner.html). A total of 126 tRNA genes were predicted using tRNAscan-SE (). The draft functional annotation was performed using Sma3S (), where the UniProt-TrEMBL (release 2015_11) and UniProt-SwissProt (release 2015_11) databases were used, resulting in 7,890 and 2,551 genes being functionally annotated by UniProt-TrEMBL and […]

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Draft Genome Sequence of the Causative Antigen of Summer Type Hypersensitivity Pneumonitis, Trichosporon domesticum JCM 9580

2016
Genome Announc
PMCID: 4939788
PMID: 27389271
DOI: 10.1128/genomeA.00651-16
call_split See protocol

[…] 31.8), together with Augustus (3.0.3) and SNAP (2013-02-16), both of which were trained with the Cryptococcus neoformans var. neoformans JEC21 sequence, and GeneMark-ES (4.21) (), and annotated using Sma3s (). The T. domesticum JCM 9580 genome comprised 28 scaffolds (93 contigs) with a total size of 26.6 Mbp (204× coverage, 0.1% gaps). Annotation of the genome resulted in a set of 8,170 protein-co […]

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Sma3s institution(s)
Centro Andaluz de Biolog ́ıa del Desarrollo (CABD-CSIC-JA), Universidad Pablo de Olavide, Sevilla, Spain; CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairao, Portugal
Sma3s funding source(s)
Supported by the Ministry of Economyand Competitiveness of the Spanish Government grant BFU2013-46923-P.

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