Biology subjects

Borodovsky, M.

Publications and source records attributed to Borodovsky, M..

11 recordsLinked to original sources

bioRxiv2026

HPVarcall: Calling lineages and sublineages for partial DNA sequences of human papillomavirus

We describe a computational method, HPVarcall, that assigns DNA sequences of a human papillomavirus (HPV) variant of known type to lineages and sublineages. The algorithm relies on statistical models - positional frequency profiles - trained on multiple alignments of HPV genomic sequences that are known to belong to specific sublineages of a given HPV type. The workflow begins with multiple alignment of all available sequences for the HPV type, followed by construction of a phylogenetic tree and identification of branches containing sublineage-specific reference sequences. In the prediction phase, sublineage-specific statistical models are used to compute the posterior probabilities for each sublineage given a query sequence. The query classifies to belong to the sublineage with the highest posterior probability. Accuracy assessments performed for the nine HPV types included in the Gardasil 9 vaccine demonstrated a low error rate in assigning HPV genomic fragments of at least 1000 nucleotides to their correct sublineages and even higher accuracy for longer sequence fragments.

bioinformatics↗

bioRxiv2023

BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA

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 evidence available from transcriptomes and proteomes vary across genomes, between genes and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement was made by the recently released GeneMark-ETP integrating all three data types. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperformed BRAKER1 and BRAKER2. The average transcript-level F1-score was increased by[~] 20 percentage points on average, while the difference was most pronounced for species withlarge and complex genomes. BRAKER3 also outperformed other existing tools, MAKER2, Funannotate and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

bioinformatics↗

bioRxiv2023

GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistence with Extrinsic Data

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-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data is sufficient for making gene predictions with high confidence. The genes situated in the genomic space between the high confidence genes are predicted in the next stage. The set of high confidence genes serves as an initial training set for the statistical model. Further on, the model parameters are iteratively updated in the rounds of gene prediction and parameter re-estimation. Upon reaching convergence, GeneMark-ETP makes the final predictions and delivers the whole complement of predicted genes. GeneMark-ETP outperformed gene finders using a single type of extrinsic evidence. Comparisons with gene finders utilizing both transcript- and protein-derived extrinsic evidence, MAKER2, and TSEBRA, demonstrated that GeneMark-ETP delivered state-of-the-art gene prediction accuracy with the margin of outperforming existing approaches increasing in its applications to larger and more complex eukaryotic genomes.

bioinformatics↗

bioRxiv2022

MetaGeneMark-2: Improved Gene Prediction in Metagenomes

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 assumed that initiation of translation in prokaryotes is controlled by a ribosome binding site (RBS), a sequence with the Shine-Dalgarno (SD) consensus situated in the 5 UTR. However, [~]30% of the 5,007 genomes, representing the RefSeq collection of prokaryotic genomes, have either non-SD RBS sequences or no RBS site due to physical absence of the 5 UTR (the case of leaderless transcription). Predictions of the gene 3 ends are much more accurate; still, errors could occur due to the use of incorrect genetic code. Hence, an effective gene finding algorithm would identify true genetic code in a process of the sequence analysis. In this work prediction of gene starts was improved by inferring the GC content dependent generating functions for RBS sequences as well as for promoter sequences involved in leaderless transcription. An additional feature of the algorithm was the ability to identify alternative genetic code defined by a reassignment of the TGA stop codon (the only stop codon reassignment type known in prokaryotes). It was demonstrated that MetaGeneMark-2 made more accurate gene predictions in metagenomic sequences than several existing state-of-the-art tools.

bioinformatics↗

bioRxiv2022

Annotation of Phage Genomes with Multiple Genetic Codes

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 used in the remaining genome sections. Essentially, the phage genomes were divided into distinct blocks where one or another code was used. We have developed a tool, Mgcod, that identifies blocks with specific genetic codes and annotates protein-coding regions. We used Mgcod to scan a large set of human metagenomic contigs. As a result, we identified hundreds of contigs of viral origin with the standard genetic code used in some parts while genetic codes with opal or amber stop codon reassignments were used in others. Many of these contigs originated from known crAssphages. Further investigation revealed that while the genes in one genomic block could be translated by a distinct genetic code, translation of genes by either of the two genetic codes genes in an adjacent block would produce proteins with little difference from each other. The dual-coded genes were enriched with early-stage phage genes, while a single code was used for the late-stage genes. The code-block structure expands the phages ability to infect bacteria whose genomes employ the standard genetic code. The new tool provides means for accurate annotation of unusual genomes of these phages.

bioinformatics↗

bioRxiv2022

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist)

BackgroundBlackberries (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 raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. FindingsHere we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession Hillquist (R. argutus). Hillquist is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The Hillquist assembly, generated using PacBio long reads scaffolded with Hi-C sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on seven chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted using the assembly and Iso-Seq and RNA-seq data, of which 72% were functionally annotated. ConclusionsThe utility of the Hillquist genome has been demonstrated here by the development of the first genotyping-by-sequencing based linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.

genomics↗

bioRxiv2021

TSEBRA: Transcript Selector for BRAKER

BackgroundBRAKER 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 and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited. ResultsWe present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler. ConclusionTSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.

bioinformatics↗

bioRxiv2020

StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence

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 most accurate tools. To address this discrepancy, we have introduced StartLink+, an approach combining ab initio and multiple sequence alignment based methods. StartLink+ makes predictions for a majority of genes per genome (73% on average); in tests on sets of genes with experimentally verified starts the StartLink+ accuracy was shown to be 98-99%. When StartLink+ predictions made for a large set of prokaryotic genomes were compared with the database annotations we observed that on average the gene start annotations deviated from the predictions for ~5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes.

bioinformatics↗

bioRxiv2020

BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database

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 generate genes coordinates with support of transcriptomic data. Here, we introduce BRAKER2, a pipeline with GeneMark-EP+ and AUGUSTUS externally supported by cross-species protein sequences aligned to the genome. Among the challenges addressed in the development of the new pipeline was generation of reliable hints to the locations of protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. Under equal conditions, the gene prediction accuracy of BRAKER2 was shown to be higher than the one of MAKER2, yet another genome annotation pipeline. Also, in comparison with BRAKER1 supported by a large volume of transcript data, BRAKER2 could produce a better gene prediction accuracy if the evolutionary distances to the reference species in the protein database were rather small. All over, our tests demonstrated that fully automatic BRAKER2 is a fast and accurate method for structural annotation of novel eukaryotic genomes.

bioinformatics↗

bioRxiv2020

GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins

We have made several steps towards 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 iterative unsupervised mode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads. Now we describe GeneMark-EP, a tool that utilizes another source of external information, a protein database, readily available prior to a start of a sequencing project. A new specialized pipeline, ProtHint, initiates massive protein mapping to genome and extracts hints to splice sites and translation start and stop sites of potential genes. GeneMark-EP uses the hints to improve estimation of model parameters as well as to adjust co-ordinates of predicted genes if they disagree with the most reliable hints (the -EP+ mode). Tests of GeneMark-EP and -EP+ demonstrated improvements in gene prediction accuracy in comparison with GeneMark-ES, while the GeneMark-EP+ showed higher accuracy than GeneMark-ET. We have observed that the most pronounced improvements in gene prediction accuracy happened in large eukaryotic genomes.

bioinformatics↗

bioRxiv2017

Improved Prokaryotic Gene Prediction Yields Insights into Transcription and Translation Mechanisms on Whole Genome Scale

In a conventional view of the prokaryotic genome organization promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS-2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed heuristic models designed to identify harder-to-detect genes (likely horizontally transferred). Importantly, we designed GeneMarkS-2 to identify several types of distinct sequence patterns (signals) involved in gene expression control, among them the patterns characteristic for leaderless transcription as well as non-canonical RBS patterns. To assess the accuracy of GeneMarkS-2 we used genes validated by COG annotation, proteomics experiments, and N-terminal protein sequencing. We observed that GeneMarkS-2 performed better on average in all accuracy measures when compared with the current state-of-the-art gene prediction tools. Furthermore, the screening of [~]5,000 representative prokaryotic genomes made by GeneMarkS-2 predicted frequent leaderless transcription in both archaea and bacteria. We also observed that the RBS sites in some species with leadered transcription did not necessarily exhibit the Shine-Dalgarno consensus. The modeling of different types of sequence motifs regulating gene expression prompted a division of prokaryotic genomes into five categories with distinct sequence patterns around the gene starts.\n\n[Supplemental material is available for this article].

genomics↗