Mark Borodovsky
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View article: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes Open
Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic-, and protein-de…
View article: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA Open
Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the ev…
View article: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA Open
Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the ev…
View article: A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes Open
Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic- and protein-der…
View article: A chromosome-length genome assembly and annotation of blackberry ( <i>Rubus argutus</i> , cv. “Hillquist”)
A chromosome-length genome assembly and annotation of blackberry ( <i>Rubus argutus</i> , cv. “Hillquist”) Open
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red ras…
MetaGeneMark-2: Improved Gene Prediction in Metagenomes Open
Accurate prediction of protein-coding genes in metagenomic contigs presents a well-known challenge. Particularly difficult is to identify short and incomplete genes as well as positions of translation initiation sites. It is frequently ass…
View article: Annotation of Phage Genomes with Multiple Genetic Codes
Annotation of Phage Genomes with Multiple Genetic Codes Open
Some of recently discovered in human gut microbiome highly divergent crAssphages were reported to use multiple genetic codes. Opal or amber stop codon reassignments were present in parts of the genomes, while the standard genetic code was …
View article: A chromosome-length genome assembly and annotation of blackberry ( <i>Rubus argutus</i> , cv. ‘Hillquist’)
A chromosome-length genome assembly and annotation of blackberry ( <i>Rubus argutus</i> , cv. ‘Hillquist’) Open
Background Blackberries ( Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus , including black raspberry ( R. occident…
StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes Open
State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3′ends. Nonetheless, predictions of gene starts would not matc…
View article: TSEBRA: Transcript Selector for BRAKER
TSEBRA: Transcript Selector for BRAKER Open
Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence…
GeneMark-HM: improving gene prediction in DNA sequences of human microbiome Open
Computational reconstruction of nearly complete genomes from metagenomic reads may identify thousands of new uncultured candidate bacterial species. We have shown that reconstructed prokaryotic genomes along with genomes of sequenced micro…
View article: BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database Open
The task of eukaryotic genome annotation remains challenging. Only a few genomes could serve as standards of annotation achieved through a tremendous investment of human curation efforts. Still, the correctness of all alternative isoforms,…
View article: Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) Open
The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 108 synchronized meiocytes, and can be manipulate…
StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence Open
Algorithms of ab initio gene finding were shown to make sufficiently accurate predictions in prokaryotic genomes. Nonetheless, for up to 15-25% of genes per genome the gene start predictions might differ even when made by the supposedly mo…
BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database Open
Full automation of gene prediction has become an important bioinformatics task since the advent of next generation sequencing. The eukaryotic genome annotation pipeline BRAKER1 had combined self-training GeneMark-ET with AUGUSTUS to genera…
Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine Open
We recently developed a test based on the Agilent SureSelect target enrichment system capturing genomic fragments from 191 human papillomaviruses (HPV) types for Illumina sequencing. This enriched whole genome sequencing (eWGS) assay provi…
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins Open
We have made several steps toward creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient ab initio gene finding, GeneMark-ES, with parameters trained in iter…
View article: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
View article: Additional file 8 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file 8 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file 8:Pt unigenes whose EST counts in the various spore stages correlate with EST counts of U. maydis homologs in equivalent cell types/spore stages. (XLS 46 KB)
View article: Additional file 5 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file 5 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file 5:Annotation results. This table holds the most-likely annotation of 2,551 unigenes based on searches against several databases. Source of the EST and number of independent sequences from various stages is indicated as are …
View article: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
View article: Additional file 6 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file 6 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file 6:Pt unigene sequences matching U. maydis ESTs. The file shows possible homologs between the two species and their representation over the various cDNA libraries (life cycle stages). (XLS 3 MB)
View article: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
View article: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
View article: Additional file 7 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file 7 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results. (XLS 197 KB)
View article: Additional file 9 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
Additional file 9 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Open
Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various…