GET_HOMOLOGUES protocols

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description
GET_HOMOLOGUES computational protocol

GET_HOMOLOGUES specifications

Information


Unique identifier OMICS_05365
Name GET_HOMOLOGUES
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for GET_HOMOLOGUES

GET_HOMOLOGUES IN pipelines

 (10)
2018
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] 30], we decided to involve them in this study to acquire richer information on the evolution and forces for genome changes of the group due to their relatively unique living strategies., the program get_homologues v3.0.3 [31], with three popular clustering algorithms, i.e. bidirectional best hit (bdbh), cogtriangles [32] and orthomcl [33], was used for clustering orthologous genes […]

2017
PMCID: 5216340
PMID: 28057934
DOI: 10.1038/srep40206

[…] and assembled using spades 3.6.226. the final assemblies were filtered to contain ≥200 bp contigs. genome annotation was performed using prokka 1.1127. pan genome analysis was performed by get_homologues software28, using the standard described by tettelin and collaborators29., the whole genome sequences of 17 strains achieved from our study and 42 strains available in ncbi genome […]

2017
PMCID: 5289962
PMID: 28217118
DOI: 10.3389/fmicb.2017.00132

[…] 0.18.3; galili, 2015)., the genetic potential of individual leuconostoc lineages that were identified by the pan-/core-genome analysis was investigated by producing intra-linage pan-genomes using get_homologues (version 2.0.10). the pan-genome for each lineage was analyzed using blast2go v4 (conesa et al., 2005) to identify functionality, and geneious 8.1.8 (kearse et al., 2012) to identify […]

2017
PMCID: 5306281
PMID: 28261241
DOI: 10.3389/fpls.2017.00184

[…] genes include several examples of unknown functions, specific transposases or proteins such as prolamins, self-incompatibility s1 or c1 proteins., the results presented in this paper illustrate how get_homologues-est can be used to analyze plant pan-genomes from either genomic sequences or expressed tags. our approach overcomes some intrinsic caveats, such as incomplete sequences or transcripts […]

2017
PMCID: 5381553
PMID: 28201585
DOI: 10.1093/gbe/evx022

[…] the set of genomes used here is representative of the total genetic pool of m. bovis, we estimated pan- and core-genome curves (tettelin et al. 2005). this was done for the 38-data set using the get_homologues.pl script (contreras-moreira and vinuesa 2013) with the “–c” option and 20 resampling steps. at each resampling, genomes were included in an order different from the previous […]

GET_HOMOLOGUES institution(s)
Estación Experimental de Aula Dei (EEAD-CSIC), Zaragoza, Spain; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico

GET_HOMOLOGUES reviews

 (2)
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Bruno Contreras-Moreira

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Desktop
After reading sro's review, just wanted to add that Alvaro Rodriguez and me have recently tested length normalization as done by OrthoFinder. You can find the results at https://github.com/eead-csic-compbio/get_homologues/tree/master/user_utils/normalize

sro

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Desktop
This suit allows users to calculate pan- and core-genome for prokaryote and eukaryote genomes. It is relatively easy to use and it comes with good tutorials. It allows you to to use different algorithm to calculate orthologues genes, which I like. Moreover is periodically patched and new features are added. Moreover, it is quite interesting the features of looking for syntenic genes only, or look for orthologues intergenic regions. I would only have like to see OrthonFinder implemented and some more visualization tools for syntenic orthologues genes and pan- core-genomes. Overall it is a relly good and flexible tool! Highly recommendable.