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GASTS specifications

Information


Unique identifier OMICS_22755
Name GASTS
Alternative name Generalized Adequate Subtree Tree Scoring

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Publication for Generalized Adequate Subtree Tree Scoring

GASTS citations

 (6)
library_books

Ancestral Genome Reconstruction on Whole Genome Level

2017
Curr Genomics
PMCID: 5635614
PMID: 29081686
DOI: 10.2174/1389202918666170307120943

[…] -based and homology/adjacency-based categories. We analyze and compare their performance on simulated datasets and evaluate their outputs. For the distance/event-based approaches, we select MGRA2 and GASTS. MGRA2 is the only distance/event-based approach that could deal with all kinds of evolutionary events []. GASTS is famous for its speed and accuracy for small-scale datasets, but it could only […]

library_books

Fast ancestral gene order reconstruction of genomes with unequal gene content

2016
BMC Bioinformatics
PMCID: 5123410
PMID: 28185578
DOI: 10.1186/s12859-016-1261-9

[…] distance, many other distance-based methods were developed, with different distances, such as the reversal distance (GRAPPA [] and MGR []), the double cut and join (DCJ) distance [, ] (PATHGROUPS [], GASTS [] and MGRA [, ]), and the single cut or join (SCJ) distance [] (SCJ Small Phylogeny []), just to cite a few examples.Another category can be called homology-based, where methods usually do not […]

library_books

A transcriptome approach towards understanding the development of ripening capacity in ‘Bartlett’ pears (Pyrus communis L.)

2015
BMC Genomics
PMCID: 4600301
PMID: 26452470
DOI: 10.1186/s12864-015-1939-9

[…] a fruit [] and silique growth of Arabidopsis []. In the present study, GA-associated gene subcategories were enriched at the S1-S2 and S2-S3 transitions (Additional file ). GA-stimulated transcripts (GASTs) are known as targets of GA regulation []. Two annotated GASTs and three putative GA-regulated transcripts were up-regulated from S1 to S2 (Table ). This may indicate that GAs play a role in fru […]

library_books

Reconstruction of ancestral gene orders using intermediate genomes

2015
BMC Bioinformatics
PMCID: 4602182
PMID: 26451811
DOI: 10.1186/1471-2105-16-S14-S3

[…] dels, such as signed reversals and the Double-Cut-and-Join (DCJ) distance [,], new algorithms have been proposed. Notable examples of recent distance-based methods include MGRA [], PATHGROUPS [], and GASTS [], based on minimizing the DCJ distance, and SCJ Small Phylogeny [], based on the Single-Cut-or-Join (SCJ) model []. Since rearrangement distance problems are usually NP-hard for three or more […]

call_split

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

2014
PLoS One
PMCID: 4193752
PMID: 25302942
DOI: 10.1371/journal.pone.0108796
call_split See protocol

[…] omosomal genomic distances as its branch lengths computed by GRIMM . Moreover, in GapAdj, the cutoff value and maximal iterations were set to and as suggested by the authors. The event-based method GASTS was simply run by providing the true tree and the input genomes. Results of InferCARsPro under large tree diameters were missing as it failed to finish the tests in three days. shows the result […]

library_books

Plasmodium Protease ROM1 Is Important for Proper Formation of the Parasitophorous Vacuole

2011
PLoS Pathog
PMCID: 3164628
PMID: 21909259
DOI: 10.1371/journal.ppat.1002197

[…] sing two annotated genes on PlasmoDB, py00729 and py00728. Based on topology predictions (TMHMM and HMMTOP), PyROM1 has seven transmembrane domains with the canonical rhomboid catalytic serine motif (GASTS) found within transmembrane domain four and a conserved histidine found within transmembrane domain six (merops.sanger.ac.uk). It has an N-terminal tail of 52 amino acids that includes the conse […]

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GASTS institution(s)
Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland

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