scholarly journals Alignathon: A competitive assessment of whole genome alignment methods.

2014 ◽  
Author(s):  
Dent Earl ◽  
Ngan K Nguyen ◽  
Glenn Hickey ◽  
Robert S. Harris ◽  
Stephen Fitzgerald ◽  
...  
Keyword(s):  
Genome Alignment ◽  
Whole Genome ◽  
Alignment Quality ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Simulation Based ◽  
Benchmark Datasets ◽  
Whole Genome Alignment

Background: Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole genome alignment (WGA). Results: Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments, and assessments were performed collectively after all the submissions were received. Three datasets were used: two of simulated primate and mammalian phylogenies, and one of 20 real fly genomes. In total 35 submissions were assessed, submitted by ten teams using 12 different alignment pipelines. Conclusions: We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable difference in the alignment quality of differently annotated regions, and found few tools aligned the duplications analysed. We found many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all datasets, submissions and assessment programs for further study, and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.

scholarly journals A statistical score for assessing the quality of multiple sequence alignments

2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Virpi Ahola ◽  
Tero Aittokallio ◽  
Mauno Vihinen ◽  
Esa Uusipaikka
Keyword(s):  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

scholarly journals Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark

2009 ◽  
Vol 19 (4) ◽  
pp. 675-678 ◽  
Author(s):  
Jacek Błażewicz ◽  
Piotr Formanowicz ◽  
Paweł Wojciechowski
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Formal Definitions ◽  
Accuracy Measures ◽  
Total Column ◽  
Better Than

Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmarkBAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured bybali_score—an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated bybali_scoreare different from those obtained on the basis of the formal definitions of the measures. We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.

scholarly journals Panaconda: Application of pan-synteny graph models to genome content analysis

2017 ◽  
Author(s):  
Andrew S. Warren ◽  
James J. Davis ◽  
Alice R. Wattam ◽  
Dustin Machi ◽  
João C. Setubal ◽  
...  
Keyword(s):  
Gene Families ◽  
De Bruijn Graph ◽  
Genome Alignment ◽  
Whole Genome ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
Link Type ◽  
De Bruijn ◽  
Similarities And Differences ◽  
Whole Genome Alignment

AbstractMotivationWhole-genome alignment and pan-genome analysis are useful tools in understanding the similarities and differences of many genomes in an evolutionary context. Here we introduce the concept of pan-synteny graphs, an analysis method that combines elements of both to represent conservation and change of multiple prokaryotic genomes at an architectural level. Pan-synteny graphs represent a reference free approach for the comparison of many genomes and allows for the identification of synteny, insertion, deletion, replacement, inversion, recombination, missed assembly joins, evolutionary hotspots, and reference based scaffolding.ResultsWe present an algorithm for creating whole genome multiple sequence comparisons and a model for representing the similarities and differences among sequences as a graph of syntenic gene families. As part of the pan-synteny graph creation, we first create a de Bruijn graph. Instead of the alphabet of nucleotides commonly used in genome assembly, we use an alphabet of gene families. This de Bruijn graph is then processed to create the pan-synteny graph. Our approach is novel in that it explicitly controls how regions from the same sequence and genome are aligned and generates a graph in which all sequences are fully represented as paths. This method harnesses previous computation involved in protein family calculation to speed up the creation of whole genome alignment for many genomes. We provide the software suite Panaconda, for the calculation of pan-synteny graphs given annotation input, and an implementation of methods for their layout and visualization.AvailabilityPanaconda is available at https://github.com/aswarren/pangenome_graphs and datasets used in examples are available at https://github.com/aswarren/pangenome_examplesContactAndrew Warren [email protected]

scholarly journals Boosting alignment accuracy through adaptive local realignment

2016 ◽  
Author(s):  
Dan DeBlasio ◽  
John Kececioglu
Keyword(s):  
New Method ◽  
Alignment Accuracy ◽  
Global Alignment ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Local Realignment ◽  
First Time ◽  
Final Alignment

AbstractMotivationWhile mutation rates can vary across the residues of a protein, when computing alignments of protein sequences the same setting of values for substitution score and gap penalty parameters is typically used across their entire length. We provide for the first time a new method called adaptive local realignment that automatically uses diverse parameter settings in different regions of the input sequences when computing multiple sequence alignments. This allows parameter settings to adapt to more closely match the local mutation rate across a protein.MethodOur method builds on our prior work on global alignment parameter advising with the Facet alignment accuracy estimator. Given a computed alignment, in each region that has low estimated accuracy, a collection of candidate realignments is generated using a precomputed set of alternate parameter settings. If one of these alternate realignments has higher estimated accuracy than the original subalignment, the region is replaced with the new realignment, and the concatenation of these realigned regions forms the final alignment that is output.ResultsAdaptive local realignment significantly improves the quality of alignments over using the single best default parameter setting. In particular, this new method of local advising, when combined with prior methods for global advising, boosts alignment accuracy by as much as 26% over the best default setting on hard-to-align benchmarks (and by 6.4% over using global advising alone).AvailabilityA new version of the Opal multiple sequence aligner that incorporates adaptive local realignment using Facet for parameter advising, is available free for non-commercial use at http://[email protected]

scholarly journals Positive natural selection in primate genes of the type I interferon response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elena N. Judd ◽  
Alison R. Gilchrist ◽  
Nicholas R. Meyerson ◽  
Sara L. Sawyer
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Interferon Stimulated Genes ◽  
Interferon Induction

Abstract Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one. Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.

scholarly journals Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis

2021 ◽  
Author(s):  
Roman Kotłowski ◽  
Alicja Nowak-Zaleska ◽  
Grzegorz Węgrzyn
Keyword(s):  
Acinetobacter Baumannii ◽  
Time Frame ◽  
Repeated Sequences ◽  
Hospital Environment ◽  
Genome Alignment ◽  
Whole Genome ◽  
Differential Analysis ◽  
Gene Encoding ◽  
Resistance Patterns ◽  
Whole Genome Alignment

AbstractAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation in the gene encoding the EmrA-homologue of E. coli, and antibiotic resistance patterns, in combination with three newly identified polymorphic regions in the genomes of A. baumannii clinical isolates. Differential analysis of two similarity matrices between different genotypes and resistance patterns allowed to distinguish three significant correlations (p < 0.05) between 172 bp DNA insertion combined with resistance to chloramphenicol and gentamycin. Interestingly, 45 and 55 bp DNA insertions within the CRISPR region were identified, and combined during analyses with resistance/susceptibility to trimethoprim/sulfamethoxazole. Moreover, 184 or 1374 bp DNA length polymorphisms in the genomic region located upstream of the GTP cyclohydrolase I gene, associated mainly with imipenem susceptibility, was identified. In addition, considerable nucleotide polymorphism of the gene encoding the gamma/tau subunit of DNA polymerase III, an enzyme crucial for bacterial DNA replication, was discovered. The differentiation analysis performed using the above described approach allowed us to monitor the distribution of A. baumannii isolates in different wards of the hospital in the time frame of several years, indicating that the optimized method may be useful in hospital epidemiological studies, particularly in identification of the source of primary infections.

Sign in / Sign up

Export Citation Format

Share Document