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TIGRFAMs specifications

Information


Unique identifier OMICS_01700
Name TIGRFAMs
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/TIGRFAMs

Maintainer


  • person_outline Daniel H. Haft

Publication for TIGRFAMs

TIGRFAMs citations

 (146)
library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] le-specific GA (gathering) thresholds. Furthermore, the predicted secretomes in Aspergillus species were annotated with protein family and domain information from TIGRFAM (http://www.jcvi.org/cgi-bin/tigrfams/index.cgi), SFLD (http://sfld.rbvi.ucsf.edu/django/), SMART (http://smart.embl-heidelberg.de/), CDD(https://www.ncbi.nlm.nih.gov/cdd), PROSITE, SUPERFAMILY (http://supfam.org/SUPERFAMILY/), P […]

library_books

Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

2018
BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] ased on blast alignment. The gene model was predicted by Glimmer [] and compared with the following public databases: COGs [], Interpro [], Pfam [], Prints [], PROSITE [], Smart [], Swissprot [], and Tigrfams []. Tblastx [] was used to reanalyze intergenic regions for ORFs. Hmmer [] on pfam 5.4 was used for motif analysis. Stringent parameters were used to identify tRNAs by trnascan-se [] and ribo […]

library_books

Alignment free clustering of large data sets of unannotated protein conserved regions using minhashing

2018
BMC Bioinformatics
PMCID: 5838936
PMID: 29506470
DOI: 10.1186/s12859-018-2080-y

[…] ery protein they compare this sequence with the constructed models and place it in the family that gives the best match. Examples of these methods are Pfam [, ], SMART [, ], PROSITE [], PRINTS [] and TIGRFAMs [].On the other hand, there are a few methods that try to automatically generate conserved regions or an estimate of these regions and perform the clustering based on them. These methods are […]

library_books

Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs

2018
Genome Biol Evol
PMCID: 5822708
PMID: 29420776
DOI: 10.1093/gbe/evy033

[…] Ammer () for ribosomal genes, Aragorn () for tRNAs, SignalP () for signal peptides, and Infernal () for noncoding RNAs. Functional annotation was performed in Prokka with the UniProt (), Pfam (), and TIGRFAMs () databases. Additional functional annotation was performed using the KEGG () and COG () databases with KAAS () and cdd2cog (), respectively. Genomes and annotations were inspected and manua […]

library_books

Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum

2018
Genes
PMCID: 5852556
PMID: 29364862
DOI: 10.3390/genes9020060

[…] M (TMHMM), SignalP, and PROSITE matches. Several types of annotation are attached to each protein based on the available evidence, including: Enzyme Commission (EC) numbers, Gene Ontology (GO) terms, TIGRfams, and protein names. […]

library_books

The Ancient Link between G Protein Coupled Receptors and C Terminal Phospholipid Kinase Domains

2018
MBio
PMCID: 5784254
PMID: 29362235
DOI: 10.1128/mBio.02119-17

[…] searches in the Uniprot database using keywords and protein domain identifiers. All potential candidates were analyzed for protein domain composition using the SMART database () and Pfam, Prints, and TIGRFAMs under InterProScan (). TM domains were predicted using Phobius (), TMHMM (), HMMTOP (), GPCRHMM (), and SOSUI (). Proteins containing domains other than PIPK at the C terminus and those witho […]

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TIGRFAMs institution(s)
Informatics, J Craig Venter Institute, Chinakville, MD, USA

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