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GORBI: Gene Ontology at Rudjer Boskovic Institute :: Search

GORBI contains millions of predicted gene functions for 900 Bacteria and Archaea. You can search the database by the genome of interest, or by a particular Gene Ontology category, or by individual genes. GORBI examines presence/absence patterns. Of gene orthologs and paralogs. Across prokaryotic genomes. We use machine learning. Infer new GO annotations for genes. 13 million annotations were made at a stringent FDR 10%. We validated 38 predictions. Query by Gene Ontology:. Helicobacter pylori ATCC 700392.

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GORBI: Gene Ontology at Rudjer Boskovic Institute :: Search | gorbi.irb.hr Reviews

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GORBI contains millions of predicted gene functions for 900 Bacteria and Archaea. You can search the database by the genome of interest, or by a particular Gene Ontology category, or by individual genes. GORBI examines presence/absence patterns. Of gene orthologs and paralogs. Across prokaryotic genomes. We use machine learning. Infer new GO annotations for genes. 13 million annotations were made at a stringent FDR 10%. We validated 38 predictions. Query by Gene Ontology:. Helicobacter pylori ATCC 700392.

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1 method

2 help / about

3 8150 biological process

4 5575 cellular component

5 3674 molecular function

6 2 bacteria

7 to accurately

8 experimentally in

9 e coli

10 suggesting that our

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method,help / about,8150 biological process,5575 cellular component,3674 molecular function,2 bacteria,to accurately,experimentally in,e coli,suggesting that our,confidence estimates,are correct,example #1,metal cluster binding,browse gene ontology,high

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GORBI: Gene Ontology at Rudjer Boskovic Institute :: Search | gorbi.irb.hr Reviews

https://gorbi.irb.hr

GORBI contains millions of predicted gene functions for 900 Bacteria and Archaea. You can search the database by the genome of interest, or by a particular Gene Ontology category, or by individual genes. GORBI examines presence/absence patterns. Of gene orthologs and paralogs. Across prokaryotic genomes. We use machine learning. Infer new GO annotations for genes. 13 million annotations were made at a stringent FDR 10%. We validated 38 predictions. Query by Gene Ontology:. Helicobacter pylori ATCC 700392.

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gorbi.irb.hr

1

GORBI: Gene Ontology at Rudjer Boskovic Institute :: Estimating the confidence of annotations

http://gorbi.irb.hr/en/method/calculating-the-confidence-of-annotations

Growth of sequence databases. OMA orthologs and paralogs. Enriching profiles with paralogs. Estimating the confidence of annotations. Experimental validation in E. coli. Estimating the confidence of annotations. When estimating the classification error, RF uses the bagging ( B. Methodology of resampling the dataset (Breiman, 2001). One bootstrap sample consists of the same number of examples as the original dataset, randomly drawn. Consequently, this contains 2/3 of unique examples. In addition to this r...

2

GORBI: Gene Ontology at Rudjer Boskovic Institute :: Hierarchical multi-label classification

http://gorbi.irb.hr/en/method/hierarchical-multi-label-classification

Growth of sequence databases. OMA orthologs and paralogs. Enriching profiles with paralogs. Estimating the confidence of annotations. Experimental validation in E. coli. In order to predict GO annotations of OMA orthologous groups,. We employed the machine learning algorithm CLUS-HMC, based on decision trees for Hierarchical Multi-label Classification. The CLUS-HMC decision trees are able to deal with multiple, hierarchically organized class labels. In our case, these are GO annotations of genes. Compari...

3

GORBI: Gene Ontology at Rudjer Boskovic Institute :: Help / About

http://gorbi.irb.hr/en/help

The people behind GORBI. Please follow the links in the left sidebar for more information on specific topics. For any questions not covered in the FAQ, for comments or requests, please write to. GORBI: Gene Ontology at Ruđer Bošković Institute. By http:/ gorbi.irb.hr. Is licensed under a Creative Commons Attribution-Non-Commercial-Share Alike 3.0 Croatia License.

4

GORBI: Gene Ontology at Rudjer Boskovic Institute :: Method

http://gorbi.irb.hr/en/method

Growth of sequence databases. OMA orthologs and paralogs. Enriching profiles with paralogs. Estimating the confidence of annotations. Experimental validation in E. coli. Phylogenetic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. While the number of sequenced prokaryotic genomes grows rapidly, the number of assignments of gene functions in the available databases remain low. And 800 such annotations for. For orthology and paralogy-aware. GORBI: Gene Ontology at R...

5

GORBI: Gene Ontology at Rudjer Boskovic Institute :: Experimental validation in E. coli

http://gorbi.irb.hr/en/method/experimental-validation

Growth of sequence databases. OMA orthologs and paralogs. Enriching profiles with paralogs. Estimating the confidence of annotations. Experimental validation in E. coli. Experimental validation of the model's accuracy estimates. To validate how realistic are the confidence estimates reported. By our machine learning model. We chose annotations for 38 genes in. K-12 at a threshold of 60% expected Precision. Response to DNA damage stimulus,. Peptidoglycan-based cell wall biogenesis. Mutant had 7% survival ...

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revigo.irb.hr

About Revigo

http://revigo.irb.hr/about_hr.jsp

O serveru REVIGO: motivacija i ciljevi. Ontologije su strukturirani načini pohrane znanja, i pokazale su svoju upotrebljivost u raznim područjima znanosti i industrije. Istaknuti primjer je tzv. Gene Ontology, koja je istraživačima iz svih polja biologije pružila kontrolirani vokabular za opis funkcija genskih produkata - proteina. Za daljnje informacije, molimo pišite na adresu:. Ako vam je REVIGO bio koristan u istraživanju, molim citirajte sljedeću referencu: Supek F et al. ". A Java implementation of...

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GORBI: Gene Ontology at Rudjer Boskovic Institute :: Search

GORBI contains millions of predicted gene functions for 900 Bacteria and Archaea. You can search the database by the genome of interest, or by a particular Gene Ontology category, or by individual genes. GORBI examines presence/absence patterns. Of gene orthologs and paralogs. Across prokaryotic genomes. We use machine learning. Infer new GO annotations for genes. 13 million annotations were made at a stringent FDR 10%. We validated 38 predictions. Query by Gene Ontology:. Helicobacter pylori ATCC 700392.

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