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SIFTER specifications

Information


Unique identifier OMICS_08524
Name SIFTER
Alternative name Statistical Inference of Function Through Evolutionary Relationships
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Uniprot ID or Accession, Go term ID, Function name, Species Name or ID, etc.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Steven E. Brenner

Information


Unique identifier OMICS_08524
Name SIFTER
Alternative name Statistical Inference of Function Through Evolutionary Relationships
Interface Web user interface
Restrictions to use None
Input data Uniprot ID or Accession, Go term ID, Function name, Species Name or ID, etc.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Steven E. Brenner

Publications for Statistical Inference of Function Through Evolutionary Relationships

SIFTER citations

 (4)
library_books

HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

2018
PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] oherence index, also based on SDPs. CDD [] is a domain database that includes an automated hierarchical classification of subfamilies, based on Bayesian analysis of what basically constitute SDPs []. Sifter [,] uses an empirical Bayesian approach to combine function evidence from for the Gene Ontology Annotation (GOA) [] database with a phylogenetic tree. Panther [] is a database with curated prot […]

library_books

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

2015
Int J Mol Sci
PMCID: 4691145
PMID: 26694353
DOI: 10.3390/ijms161226202

[…] se methods have been developed as rapid methods that utilize sequence information only. The majority of methods predict function based on Gene Ontology (GO) terms (which include: INGA [], EFI-EST [], SIFTER [], GEO2Enrichr [], PANNZER [], and PILL []) with fewer utilizing EC numbers (EFI-EST [] and DomSign []) for functional annotation. Furthermore, a number of structure-based methods for the pred […]

library_books

Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: Recurrence of tyrosine aminotransferase activity in the Iα subfamily

2013
Proteins
PMCID: 3823064
PMID: 23671031
DOI: 10.1002/prot.24318

[…] We ran SIFTER on the phylogenetic tree for the aminotransferase Iα family containing 92 sequences (see Materials and Methods). In all experiments on this family, there were exactly two candidate functions fr […]

library_books

Protein Molecular Function Prediction by Bayesian Phylogenomics

2005
PLoS Comput Biol
PMCID: 1246806
PMID: 16217548
DOI: 10.1371/journal.pcbi.0010045

[…] e similarity, such as a BLAST E-value, as an indicator of homology. A functional annotation is heuristically transferred to the query sequence based on reported functions of similar sequences.SIFTER (Statistical Inference of Function Through Evolutionary Relationships) takes a different approach to function annotation. Phylogenetic information, if leveraged correctly, addresses many of the weaknes […]

Citations

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SIFTER institution(s)
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA

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