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Information


Unique identifier OMICS_20984
Name AntiFam
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 1.0
Maintained Yes

Maintainer


  • person_outline Ruth Eberhardt

Publication for AntiFam

AntiFam citations

 (5)
library_books

Gene Unprediction with Spurio: A tool to identify spurious protein sequences

2018
F1000Res
PMCID: 5897793
PMID: 29721311
DOI: 10.5256/f1000research.15280.r31447

[…] .Here we describe two examples that illustrate the concept of identifying spurious proteins by inspecting homologous DNA sequence. The first example is from a known spurious protein identified by the AntiFam resource. This protein is an uncharacterized protein from the microbe Acinetobacter bereziniae (UniProt accession: N8YUQ2) which was revealed to be a translated CRISPR YPRES repeat sequence. I […]

library_books

Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals

2016
PMCID: 4830120
PMID: 27074260
DOI: 10.1590/0074-02760160010

[…] each strain the de novo assemblies were merged using CISA ( and evaluated using QUAST (. Genome annotation was performed as previous described ( using Prodigal (, NCBI-BLAST+ (, , Uniprot (, HMMER (, AntiFam (, tRNAscan-SE (, RNAmmer (, INFERNAL (, Aragorn (, and Rfam (, and manually reviewed using Artemis (. In silico multilocus sequence typing (MLST) was performed using BLASTn from the NCBI-BLAS […]

library_books

Draft Genome Sequences of Leptospira santarosai Strains U160, U164, and U233, Isolated from Asymptomatic Cattle

2015
Genome Announc
PMCID: 4536688
PMID: 26272577
DOI: 10.1128/genomeA.00910-15

[…] nnotation, open reading frames (ORFs) found by Prodigal () were aligned against a data set of proteins from the Leptospira genus from Uniprot (http://www.uniprot.org) using BLAST (, ) and against the AntiFam database () using HMMER (). The tRNAs and rRNAs were predicted using tRNAscan-SE () and RNAmmer (), respectively. For the prediction of other noncoding RNAs (ncRNAs) and regulatory sequences, […]

library_books

Expanding the catalog of cas genes with metagenomes

2013
Nucleic Acids Res
PMCID: 3936711
PMID: 24319142
DOI: 10.1093/nar/gkt1262

[…] %), and by comparisons of their profile HMMs; these seven clusters were excluded from our collection of novel Cas families. As a further quality control, we searched the remaining 24 clusters against AntiFam (which collects suspicious ORFs) and CRISPR array repeats, and no matches were found; we also checked reads coverage for the cas genes identified from HMP datasets, all indicating a low chance […]

library_books

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

2012
Biol Direct
PMCID: 3534567
PMID: 23111013
DOI: 10.1186/1745-6150-7-37

[…] r of additional points about the paper.One mechanism to evaluate COMBREX for spurious gene calls is to search it with a database of HMMs built to detect some of the most popular spurious gene calls – AntiFam. These models should be used to check both COMBREX genes with evidence and GLIMMER’s candidate missed genes.Authors’ response: We thank the reviewer for bringing AntiFam to our attention. We u […]

Citations

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AntiFam institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK; Department of Bioinformatics, J. Craig Venter Institute, Rockville, MD, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
AntiFam funding source(s)
Supported by Wellcome Trust (grant number WT077044/Z/05/Z); National Human Genome Research Institute (grant number R01 HG004881).

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