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GAML: genome assembly by maximum likelihood

Vladimír Boža, Broňa Brejová, Tomáš Vinař
2015 Algorithms for Molecular Biology  
We achieve this by searching for an assembly with the maximum likelihood in a probabilistic model capturing error rate, insert lengths, and other characteristics of the sequencing technology used to produce  ...  We have implemented a prototype genome assembler GAML that can use any combination of insert sizes with Illumina or 454 reads, as well as PacBio reads.  ...  Acknowledgements This research was funded by VEGA Grants 1/1085/12 (BB) and 1/0719/14 (TV). The authors would like to thank Viraj Deshpande for sharing his research data.  ... 
doi:10.1186/s13015-015-0052-6 pmid:26042154 pmcid:PMC4454275 fatcat:nvgmikbkjveb3ir5hmzjwyddfa

GAML: Genome Assembly by Maximum Likelihood [chapter]

Vladimír Boža, Broňa Brejová, Tomáš Vinař
2014 Lecture Notes in Computer Science  
We achieve this by searching for an assembly with the maximum likelihood in a probabilistic model capturing error rate, insert lengths, and other characteristics of the sequencing technology used to produce  ...  We have implemented a prototype genome assembler GAML that can use any combination of insert sizes with Illumina or 454 reads, as well as PacBio reads.  ...  Acknowledgements This research was funded by VEGA Grants 1/1085/12 (BB) and 1/0719/14 (TV). The authors would like to thank Viraj Deshpande for sharing his research data.  ... 
doi:10.1007/978-3-662-44753-6_10 fatcat:wntsodclnvc2zpskc3o5mnwa64

The Nbp35/ApbC homolog acts as a nonessential [4Fe‐4S] transfer protein in methanogenic archaea

Cuiping Zhao, Zhe Lyu, Feng Long, Taiwo Akinyemi, Kasidet Manakongtreecheep, Dieter Söll, William B. Whitman, David J. Vinyard, Yuchen Liu
2019 FEBS Letters  
In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S  ...  This work was also supported by funds from the Louisiana State University to YL and DJV.  ...  This work was supported by the National Science Foundation grants (MCB-1632941 to YL and MCB-1410102 to WBW) and Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences  ... 
doi:10.1002/1873-3468.13673 pmid:31709520 fatcat:46uhtxye3vg2fdoo7wbcezthua

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies

Nina Luhmann, Manuel Lafond, Annelyse Thevenin, Aida Ouangraoua, Roland Wittler, Cedric Chauve
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
ancestral genome.  ...  Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary  ...  Then we computed the weights as a likelihood of this putative gap sequence given the aDNA reads, using the GAML probabilistic model described in [25] .  ... 
doi:10.1109/tcbb.2017.2661761 pmid:28166504 fatcat:hlspievsonadbhsenfaloey7zy

Genetic and functional diversity of the multiple lungfish myoglobins

Julia Lüdemann, Angela Fago, Sven Falke, Michelle Wisniewsky, Igor Schneider, Andrej Fabrizius, Thorsten Burmester
2019 The FEBS Journal  
This work is supported by the Deutsche Forschungsgemeinschaft (BU956/19-1), CNPq Universal Program Grant 403248/2016-7 to I.S and Natur og Univers, Det Frie Forskningsr ad (grant 4181-00094 to AF).  ...  The maximum likelihood analysis was carried out using the IQ-TREE web server with the JTT substitution model [55] [56] [57] .  ...  The histidine-tag was removed by incubation with the Factor Xa protease (20 µgÁmL À1 ) for 6 h at 37°C.  ... 
doi:10.1111/febs.15094 pmid:31610084 fatcat:sphp563krfasrlz3sihvs67n7y

MOLECULAR PHYLOGENETICS OF THE BUTEONINE BIRDS OF PREY (ACCIPITRIDAE)

HEATHER R. L. LERNER, MATTHEW C. KLAVER, DAVID P. MINDELL
2008 The AUK: A Quarterly Journal of Ornithology  
Maximum-likelihood (ML) values are above nodes, following BPP and preceding maximum-parsimony (MP) bootstrap values.  ...  Maximum-likelihood (ML) values are above nodes, following BPP and preceding maximum-parsimony (MP) bootstrap values.  ...  .; however, they are not sister taxa as proposed by Amadon (). e clade including some Leucopternis spp., all Buteogallus spp., and both Harpyhaliaetus spp. shows a well-supported split between species  ... 
doi:10.1525/auk.2008.06161 fatcat:za3kninqgbhlhdiafkhiauh2ba

The SCJ small parsimony problem for weighted gene adjacencies (Extended version) [article]

Nina Luhmann, Manuel Lafond, Annelyse Thévenin, Aïda Ouangraoua, Roland Wittler, Cedric Chauve
2016 arXiv   pre-print
ancestral genome.  ...  Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary  ...  Then we computed the weights as a likelihood of this putative gap sequence given the aDNA reads, using the GAML probabilistic model described in [11] .  ... 
arXiv:1603.08819v2 fatcat:rxfwxk756baavjwlx45wdsu7ya

FastEtch: A Fast Sketch-based Assembler for Genomes

Priyanka Ghosh, Ananth Kalyanaraman
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
against many state-of-the-art genome assemblers. .  ...  De novo genome assembly describes the process of reconstructing an unknown genome from a large collection of short (or long) reads sequenced from the genome.  ...  There also exists a class of assemblers that utilize a likelihood-based approach toward assembly assessmentthese include CGAL [21] and GAML [22] .  ... 
doi:10.1109/tcbb.2017.2737999 pmid:28910776 fatcat:6yttdozncjdmzcliby3dr5xg5a

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework

Guo Liang Gan, Elijah Willie, Cedric Chauve, Leonid Chindelevitch
2019 BMC Bioinformatics  
Our work paves the way for robust strain typing in the presence of within-host heterogeneity, overcoming an essential challenge currently not addressed by any existing methodology for pathogen genomics  ...  First we process each sample individually by assigning it, for each locus in the MLST scheme, a set of alleles and a proportion for each allele.  ...  If the above 0-1 ILP has multiple optimal solutions, we resort to a likelihood based method to select one, namely GAML [17] , a probabilistic model for genome assembly.  ... 
doi:10.1186/s12859-019-3204-8 pmid:31842753 pmcid:PMC6915855 fatcat:tirmlrumqbewxj2juruijbgv7y

Detection of phenotype-specific therapeutic vulnerabilities in breast cells using a CRISPR loss-of-function screen

Anna Barkovskaya, Craig M Goodwin, Kotryna Seip, Bylgja Hilmarsdottir, Solveig Pettersen, Clint Stalnecker, Olav Engebraaten, Eirikur Briem, Channing J Der, Siver A Moestue, Thorarinn Gudjonsson, Gunhild M Maelandsmo (+1 others)
2021 Molecular Oncology  
We employed a CRISPR-Cas9 loss-of-function screen targeting a 2240-genes "druggable genome" to identify phenotype-specific vulnerabilities.  ...  The work in this manuscript was supported by the following grants: the Norwegian Research Council (Grant #239940) and the Norwegian Cancer Society (Grants #168069, #205222, and #190257), and the National  ...  For screen analysis using MAGeCK (model-based analysis of genome-wide CRISPR-Cas9 knockout), we ran MAGeCK using MLE (maximum-likelihood estimation) with treatment-deconvolved FASTQ files, normalized to  ... 
doi:10.1002/1878-0261.12951 pmid:33759347 pmcid:PMC8333781 fatcat:lo4o4rwfbnajfjntsv4ddidafy

Pharmacological characterization of novel heteromeric GluCl subtypes from C. elegans and parasitic nematodes

Nicolas Lamassiaude, Elise Courtot, Angélique Corset, Claude L Charvet, Cédric Neveu
2021 British Journal of Pharmacology  
Eurofins Genomics (Luxembourg) sequenced all constructs.  ...  Maximal likelihood phylogeny reconstruction was performed using PhyML V3.1 included in the Seaview 5.0.4 package.  ... 
doi:10.1111/bph.15703 pmid:34623639 pmcid:PMC9306661 fatcat:cj6ccjdnxraexgvqw2qgfk72ke

High Performance Phylogenetic Analysis With Maximum Parsimony on Reconfigurable Hardware

Server Kasap, Khaled Benkrid
2011 IEEE Transactions on Very Large Scale Integration (vlsi) Systems  
The currently supported maximum number of taxa is 12 but this number can be easily increased.  ...  He is the holder of various research grants from the U.K. government, the EU, and Industry, and is a recognized expert reviewer by the European Commission.  ...  Reference [8] proposes a hardware/software (HW/SW) system for solving the tree reconstruction problem using the genetic algorithm for maximum likelihood (GAML) approach which yields speed-up of 30 to  ... 
doi:10.1109/tvlsi.2009.2039588 fatcat:pkegv7vzajh2xkkoxc327z3owu

Cell reproductive patterns in the green alga Pseudokirchneriella subcapitata (=Selenastrum capricornutum) and their variations under exposure to the typical toxicants potassium dichromate and 3,5-DCP

Takahiro Yamagishi, Haruyo Yamaguchi, Shigekatsu Suzuki, Yoshifumi Horie, Norihisa Tatarazako, Tobias Isaac Baskin
2017 PLoS ONE  
reproductive patterns by which two autospores are formed by binary fission ("twoautospore type") and eight autospores are formed by multiple fission ("eight-autospore type").  ...  Although it has been reported that P. subcapitata proliferates by popularity forming four daughter cells (autospores) through multiple fission after two nuclear divisions, here, we report two additional  ...  Nucleotide substitution model selection and construction of a maximum likelihood tree were carried out by using MEGA7 [22] . GTR+G model was chosen in this analysis.  ... 
doi:10.1371/journal.pone.0171259 pmid:28152022 pmcid:PMC5289587 fatcat:mfozijepxrhotkzltkrj4ybi7e

Resurrection and characterization of ancestral CYP11A1 enzymes

Philip Hartz, Silja J. Strohmaier, Basma M. EL‐Gayar, Ammar Abdulmughni, Michael C. Hutter, Frank Hannemann, Elizabeth M. J. Gillam, Rita Bernhardt
2021 The FEBS Journal  
The extraordinary robustness of ancient mitochondrial P450s, as demonstrated by CYP11A_N1, may have allowed them to stay active when presented with incompatible electron transfer systems and resulting  ...  Acknowledgments This work was supported in part by Australian Research Council Discovery Project DP160100865 (to EMJG), by an Australian Government Research Training Program Scholarship (to SJS), and by  ...  Fig. 1 . 1 Maximum-likelihood phylogenetic tree derived from the set of CYP11 sequences used here.  ... 
doi:10.1111/febs.16054 pmid:34092040 fatcat:e5ilwn64hjdj5k2xodz2fpg2p4

Barley: Genes and chromosomes

Bodil Søgaard, Penny von Wettstein-Knowles
1987 Carlsberg Research Communications  
The presented sequence and distances in cM were derived using a maximum likelihood map estimation procedure and assigning s to the zero position.  ...  The presented sequence and distances in cM were derived using a maximum likelihood map estimation procedure and" assigning necl to the zero position.  ... 
doi:10.1007/bf02907531 fatcat:zegrlmpkm5go5ak62pm676umgm
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