Supplemental Data 1-S1. Timeline of important events shaping contemporary bioinformatics and comparative genomics. Timeline is not intended to be absolutely comprehensive of each of the observed fields, their respective histories. See footnotes for key review publications, sources in addition to those listed in Reference column. Field of contributions are color-coded accordingly: purple= computer science/engineering, blue= legislation/government action, biology= green, economic/markets= orange, academic institution= pink

Database of curated links to molecular resources, tools and databases selected on the basis of recommendations from bioinformatics experts in the field. This resource relies on input from its community of bioinformatics users for suggestions. Starting in 2003, it has also started listing all links contained in the NAR Webserver issue. The different types of information available in this portal: * Computer Related: This category contains links to resources relating to programming languages often used in bioinformatics. Other tools of the trade, such as web development and database resources, are also included here. * Sequence Comparison: Tools and resources for the comparison of sequences including sequence similarity searching, alignment tools, and general comparative genomics resources. * DNA: This category contains links to useful resources for DNA sequence analyses such as tools for comparative sequence analysis and sequence assembly. Links to programs for sequence manipulation, primer design, and sequence retrieval and submission are also listed here. * Education: Links to information about the techniques, materials, people, places, and events of the greater bioinformatics community. Included are current news headlines, literature sources, educational material and links to bioinformatics courses and workshops. * Expression: Links to tools for predicting the expression, alternative splicing, and regulation of a gene sequence are found here. This section also contains links to databases, methods, and analysis tools for protein expression, SAGE, EST, and microarray data. * Human Genome: This section contains links to draft annotations of the human genome in addition to resources for sequence polymorphisms and genomics. Also included are links related to ethical discussions surrounding the study of the human genome. * Literature: Links to resources related to published literature, including tools to search for articles and through literature abstracts. Additional text mining resources, open access resources, and literature goldmines are also listed. * Model Organisms: Included in this category are links to resources for various model organisms ranging from mammals to microbes. These include databases and tools for genome scale analyses. * Other Molecules: Bioinformatics tools related to molecules other than DNA, RNA, and protein. This category will include resources for the bioinformatics of small molecules as well as for other biopolymers including carbohydrates and metabolites. * Protein: This category contains links to useful resources for protein sequence and structure analyses. Resources for phylogenetic analyses, prediction of protein features, and analyses of interactions are also found here. * RNA: Resources include links to sequence retrieval programs, structure prediction and visualization tools, motif search programs, and information on various functional RNAs.

Overview of the NHM Informatics Intiative based around the data life cycle.

Explore the historical Whois records related to blog-bioinformatics.science (Domain). Get insights into ownership history and changes over time.

This item contains a test dataset based on Sumatran rhinoceros (Dicerorhinus sumatrensis) whole-genome re-sequencing data that we publish along with the GenErode pipeline (https://github.com/NBISweden/GenErode; Kutschera et al. 2022) and that we reduced in size so that users have the possibility to get familiar with the pipeline before analyzing their own genome-wide datasets. We extracted scaffold ‘Sc9M7eS_2_HRSCAF_41’ of size 40,842,778 bp from the Sumatran rhinoceros genome assembly (Dicerorhinus sumatrensis harrissoni; GenBank accession number GCA_014189135.1) to be used as reference genome in GenErode. Some GenErode steps require the reference genome of a closely related species, so we additionally provide three scaffolds from the White rhinoceros genome assembly (Ceratotherium simum simum; GenBank accession number GCF_000283155.1) with a combined length of 41,195,616 bp that are putatively orthologous to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with gene predictions in GTF format. The repository also contains a Sumatran rhinoceros mitochondrial genome (GenBank accession number NC_012684.1) to be used as reference for the optional mitochondrial mapping step in GenErode. The test dataset contains whole-genome re-sequencing data from three historical and three modern Sumatran rhinoceros samples from the now-extinct Malay Peninsula population from von Seth et al. (2021) that was subsampled to paired-end reads that mapped to Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’, along with a small proportion of randomly selected reads that mapped to the Sumatran rhinoceros mitochondrial genome or elsewhere in the genome. For GERP analyses, scaffolds from the genome assemblies of 30 mammalian outgroup species are provided that had reciprocal blast hits to gene predictions from Sumatran rhinoceros scaffold ‘Sc9M7eS_2_HRSCAF_41’. Further, a phylogeny of the White rhinoceros and the 30 outgroup species including divergence time estimates (in billions of years) from timetree.org is available. Finally, the item contains configuration and metadata files that were used for three separate runs of GenErode to generate the results presented in Kutschera et al. (2022). Bash scripts and a workflow description for the test dataset generation are available in the GenErode GitHub repository (https://github.com/NBISweden/GenErode/docs/extras/test_dataset_generation).

References: Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, et al. GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 2022;23:228. https://doi.org/10.1186/s12859-022-04757-0 von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, et al. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations. Nature Communications 2021;12:2393.

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Uncover historical ownership history and changes over time by performing a reverse Whois lookup for the company Swiss-Institute-of-Bioinformatics.

This FAIRsharing record describes: Poxvirus Bioinformatics Resource Center has been established to provide specialized web-based resources to the scientific community studying poxviruses. This resource is no longer being maintained. For tools and data supporting virus genomics, especially related to poxviruses and other large DNA viruses, please visit the Viral Bioinformatics site maintained by our collaborator, Chris Upton: http://virology.ca For information on virus taxonomy, please visit the ICTV web site at http://www.ictvonline.org/ For updated sequence data and analytical tools, please visit http://www.viprbrc.org

Global Bioinformatics Services market size was USD 3.12 billion in 2023 and is grow to around USD 10.87 billion by 2032 with a CAGR of roughly 14.86%.

In order to introduce students to the concept of molecular diversity, we developed a short, engaging online lesson using basic bioinformatics techniques. Students were introduced to basic bioinformatics while learning about local on-campus species diversity by 1) identifying species based on a given sequence (performing Basic Local Alignment Search Tool [BLAST] analysis) and 2) researching and documenting the natural history of each species identified in a concise write-up. To assess the student’s perception of this lesson, we surveyed students using a Likert scale and asking them to elaborate in written reflection on this activity. When combined, student responses indicated that 94% of students agreed this lesson helped them understand DNA barcoding and how it is used to identify species. The majority of students, 89.5%, reported they enjoyed the lesson and mainly provided positive feedback, including “It really opened my eyes to different species on campus by looking at DNA sequences”, “I loved searching information and discovering all this new information from a DNA sequence”, and finally, “the database was fun to navigate and identifying species felt like a cool puzzle.” Our results indicate this lesson both engaged and informed students on the use of DNA barcoding as a tool to identify local species biodiversity.

Primary Image: DNA Barcoded Specimens. Crane fly, dragonfly, ant, and spider identified using DNA barcoding.

This FASTA file is the NCBI Nt (Nucleotide) database (public domain) used for holistic metagenomic screening of ancient DNA data at the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History. We offer here the FASTA file used to construct MALT databases (https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/), which are generally too large for uploading. Please see each relevent publications that use the database for MALT database construction commands.

NCBI does not retain older versions of this database which is why this has been uploaded here. It was downloaded on 2017-10-26 12:39 from: ftp://ftp-trace.ncbi.nih.gov/blast/db/FASTA/nt.gz. The NCBI Nt database is released into the public domain as per https://www.ncbi.nlm.nih.gov/home/about/policies/.

This is the dataset accompanying the following publication: Uncovering missing pieces: Duplication and deletion history of arrestins in deuterostomes. See abstract below.

Background The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. Here we elucidated the detailed evolution of arrestins in deuterostomes.

Results Identity and number of arrestin paralogs were determined searching deuterostome genomes and gene expression data. In contrast to standard gene prediction methods, our strategy first detects exons situated on different scaffolds and then solves the problem of assigning them to the correct gene. This increases both the completeness and the accuracy of the annotation in comparison to conventional database search strategies applied by the community. The employed strategy enabled us to map in detail the duplication- and deletion history of arrestin paralogs including tandem duplications, pseudogenizations and the formation of retrogenes. The two rounds of whole genome duplications in the vertebrate stem lineage gave rise to four arrestin paralogs. Surprisingly, visual arrestin ARR3 was lost in the mammalian clades Afrotheria and Xenarthra. Duplications in specific clades, on the other hand, must have given rise to new paralogs that show signatures of diversification in functional elements important for receptor binding and phosphate sensing.

Conclusion The current study traces the functional evolution of deuterostome arrestins in unprecedented detail. Based on a precise re-annotation of the exon-intron structure at nucleotide resolution, we infer the gain and loss of paralogs and patterns of conservation, co-variation and selection.

Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Bioinformatics In IVD Testing Market valued at $97.51 Bn in 2023, and is projected to $USD 171.91 Bn by 2032, at a CAGR of 6.44% from 2023 to 2032

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world’s rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species’ evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and to evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 candidate SNPs for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, divergent selection suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine. Methods All genetic data sets within this repository represent either do novo assembly or range-wide single-nucleotide polymorphisms (SNPs) obtained using the dDocent pipeline (Puritz et al. 2014a; Puritz et al. 2014b) for the critically endangered Torrey pine (Pinus torreyana Parry). Filtering of data sets was either performed using VCFtools (Danecek et al. 2011) or customized R scripts (available upon request to the corresponding author). For details on how these datasets were generated, refer to the Materials and Methods section in the published manuscript. References: Puritz, J. B., Hollenbeck, C. M., & Gold, J. R. (2014a). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2, e431. doi:10.7717/peerj.431 Puritz, J. B., Matz, M. V, Toonen, R. J., Weber, J. N., Bolnick, D. I., & Bird, C. E. (2014b). Demystifying the RAD fad. Molecular Ecology, 23(24), 5937–5942. doi: 10.1111/mec.12965 Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … Group, 1000 Genomes Project Analysis. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. doi: 10.1093/bioinformatics/btr330

Bioinformatics sequence databases such as Genbank or UniProt contain hundreds of millions of records of genomic data. These records are derived from direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centres; their diversity and scale means that they suffer from a range of data quality issues including errors, discrepancies, redundancies, ambiguities, incompleteness and inconsistencies with the published literature. In this work, we seek to investigate and analyze the data quality of sequence databases from the perspective of a curator, who must detect anomalous and suspicious records. Specifically, we emphasize the detection of inconsistent records with respect to the literature. Focusing on GenBank, we propose a set of 24 quality indicators, which are based on treating a record as a query into the published literature, and then use query quality predictors. We then carry out an analysis that shows that the proposed quality indicators and the quality of the records have a mutual relationship, in which one depends on the other. We propose to represent record literature consistency as a vector of these quality indicators. By reducing the dimensionality of this representation for visualization purposes using principal component analysis, we show that records which have been reported as inconsistent with the literature fall roughly in the same area, and therefore share similar characteristics. By manually analyzing records not previously known to be erroneous that fall in the same area than records know to be inconsistent, we show that one record out of four is inconsistent with respect to the literature. This high density of inconsistent record opens the way towards the development of automatic methods for the detection of faulty records. We conclude that literature inconsistency is a meaningful strategy for identifying suspicious records.

Over the course of evolution, hymenopteran parasitoids have developed a close relationship with heritable viruses, sometimes integrating viral genes into their chromosomes. For example, in Drosophila parasitoids belonging to the Leptopilina genus, 13 viral genes from the Filamentoviridae family have been integrated and domesticated to deliver immunosuppressive factors to host immune cells, thereby protecting parasitoid offspring from host immune response. The present study aims to comprehensively characterize this domestication event in terms of the viral genes involved, the wasp diversity affected by this event, and its chronology. Our genomic analysis of 41 Cynipoidea wasps from six subfamilies revealed 18 viral genes that were endogenized during the early radiation of the Eucoilini+Trichoplastini clade around 75 million years ago. Wasps from this highly diverse clade develop not only from Drosophila but also from a variety of Schizophora. This event coincides with the radiation of Sc..., , , # Supplementary informations from: Dating the origin of a viral domestication event in parasitoid wasps attacking Diptera

https://doi.org/10.5061/dryad.n8pk0p35c

Description of the data and file structure

This repository contains supplementary figures from the paper "Dating the origin of a viral domestication event in parasitoid wasps attacking Diptera".

Supplementary figures :

Figures S15. Alignment of Eucoilini+Trichoplastini EVEs along with Filamentous virus genes. All plots obtained using the msa R package. TryEFV: Trybliographa Endogenous Filamentous Elements (EFV), TrEFV : Trichoplasta EFV, RhEFV : Rhoptromeris EFV, LhEFV : Leptopilina heterotoma EFV, LcEFV : Leptopilina clavipes EFV, LbEFV : Leptopilina boulardi EFV, LhFV : Leptopilina heterotoma FV (FV), LbFV : Leptopilina boulardi FV, EfFV : Encarsia formosa FV, PcFV : Psyttalia concolor FV, PoFV : Platygaster orseoliae FV, CcFV1 and CcFV2 : Cotesia congregata FV ...

Aim: Shaped by both climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few, highly specialized species. The dynamic ecological histories and spatial complexities of these habitats, however, render it challenging to reconstruct the complete biogeographic histories of their endemic taxa. Here, we leverage three species of North American Ammospiza sparrows that inhabit tidal marshes ( Ammospiza caudacuta, A. maritima, and A. n. subvirgatus) and closely related freshwater species to demonstrate the utility of whole-genome data in resolving demographic and evolutionary history as it relates to divergence and dispersal events in ephemeral ecosystems. We employ a combination of demographic and biogeographic reconstructions to shed new light on the colonization history of freshwater-saline environments in this system.

Location: North America

Taxon: Ammospiza Sparrows

Methods: We sequenced whole genomes from Ammospiza sparrows to address...

Supplementary data from Evolutionary history of major chemosensory gene families across Panarthropoda.We include the onychophoran E. rowelli transcriptome assembly and annotation, as well as the chemosensory-related gene family databases and annotations described in the article.