Orphelia protocols

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Orphelia specifications


Unique identifier OMICS_01492
Name Orphelia
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Orphelia

Orphelia in pipeline

PMCID: 3792122
PMID: 24116096
DOI: 10.1371/journal.pone.0076184

[…] , was used to visually evaluate the expression and verify the tss reads. any area of transcription that was not related to a gene was evaluated using ncbi blast® ., the metagenomic orf finding tool orphelia was used to read multiple orfs in a 700 base pair model to identify orfs when no orfs were found within the 500-nt downstream tr , ., weblogo, a web-based application that can be used […]

Orphelia in publications

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] are used for phylogenetic classification or functional annotation from sequence data where there is ample data for training. neural networks have been applied successfully to gene annotation (e.g. orphelia [] and fraggenescan []). representations (similar to word2vec [] in nlp) for protein family classification have been introduced and classified with a skip-gram neural network []. rnns show […]

PMCID: 5698827
PMID: 29250541
DOI: 10.1155/2017/4740354

[…] to identify genes in metagenomics. however, the main limitation of such markov chain models is that thousands of parameters are needed in practical use. the machine learning-based methods such as orphelia [, ], mgc [], and metagun [] often formulated the metagenomic fragments with an effective mathematical expression that can truly reflect their intrinsic correlation with the target […]

PMCID: 5337752
PMID: 28321234
DOI: 10.3389/fgene.2017.00023

[…] of metageneannotator is the rbs map output which, apart from the gene location, gives information for translation initiation mechanisms useful for the analysis of evolutionary relationships ()., orphelia is available as both a web-server and command-line tool, and uses a two-step machine learning approach. in the first step, linear discriminant analysis based on monocodon usage, dicodon […]

PMCID: 4059276
PMID: 24982662
DOI: 10.3389/fpls.2014.00209

[…] diverged from any gene that has been discovered to date. there are several tools that can be used for de novo gene prediction, including metagene (), glimmer-mg (), metagenemark (), fraggenescan (), orphelia (), and metagun (). in , many of these methods were compared using statistical simulations. the authors found that their performance varied as a function of read properties (e.g., length […]

PMCID: 3792122
PMID: 24116096
DOI: 10.1371/journal.pone.0076184

[…] of annotated orfs. it was necessary to investigate whether these tags represent sterile antisense tags or whether they could represent orfs that were missed during the annotation of genome., we used orphelia , to check the presence of the orfs near such trs. we took 3000 bases of the genome sequence downstream from the start of trs and examined the presence of orfs that are 300-nt […]

Orphelia institution(s)
Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany

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