Finding set of "core genes" for Nematoda, Trematoda and Cestoda

doi:10.1038/protex.2018.043

Method Article

Finding set of "core genes" for Nematoda, Trematoda and Cestoda

https://doi.org/10.1038/protex.2018.043

This work is licensed under a CC BY 4.0 License

This protocol has been posted on Protocol Exchange, an open repository of community-contributed protocols sponsored by Nature Portfolio. These protocols are posted directly on the Protocol Exchange by authors and are made freely available to the scientific community for use and comment.

Version 1

posted

You are reading this latest protocol version

Sets of core genes were defined for nematodes, trematodes and cestodes for use as training sets for gene prediction.

Computational biology and bioinformatics

Biotechnology

core genes

orthologous groups

protein families

helminths

nematoda

platyhelminthes

trematoda

cestoda

"Core genes" are defined as genes shared by all species in a taxonomic group. Using the protocol, sets of core genes can be identified for such a group. These can then be used as training sets for gene prediction. This method describes the construction of sets of Nematode Orthologous Groups (NOGs)¹, Trematode Orthologous Groups (TROGs) and Cestode Orthologous Groups (CEOGs).

an installation of HMMER (v2.3.2)
prerequisites for OrthoMCL² (e.g. BLAST, MySQL)

compute cluster for parallel processing of multiple steps in OrthoMCL.

Building the NOGs and TROGs:

The full proteomes of twelve nematode species, four trematode species, one cestode and several eukaryotic outgroups are clustered using OrthoMCL².
NOGs are defined as clusters containing at least one member from each of the twelve included nematode species.
TROGs are defined as clusters containing at least one member from each of the four included trematode species.
An HMM is built for each cluster using HMMER (v2.3.2)³ which can be used for training gene prediction software.

For the associated publication, the CEOGs were defined using a different set of cluster input since the OrthoMCL input for the steps above only include a single cestode:

The full proteomes of four cestode species and several eukaryotic outgroups were clustered using OrthoMCL.
CEOGs are the groups containing at least one member from each of the four included cestode species.
An HMM is built for each clustering using HMMER (v2.3.2)³ which can be used for training gene prediction software.

Sets of HMM models for core genes of Nematoda, Trematoda and Cestoda which can be used for training gene prediction software.

Mitreva, M. et al. The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet 43, 228-235, doi:10.1038/ng.769 (2011).
Li, L., Stoeckert, C. J., Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178-2189, doi:10.1101/gr.1224503 (2003).
"HMMER URL":http://hmmer.org/

none

Download PDF

Version 1

posted

You are reading this latest protocol version

Finding set of "core genes" for Nematoda, Trematoda and Cestoda

Status:

Version 1

Abstract

Introduction

Reagents

Equipment

Procedure

Anticipated Results

References

Additional Declarations

Status:

Version 1

Privacy Policy

Terms of Service

Finding set of "core genes" for Nematoda, Trematoda and Cestoda

Status:

Version 1

Abstract

Introduction

Reagents

Equipment

Procedure

Anticipated Results

References

Additional Declarations

Status:

Version 1

Privacy Policy

Terms of Service

Manage Cookie Preferences