scholarly journals ASM-Clust: classifying functionally diverse protein families using alignment score matrices

2019 ◽  
Author(s):  
Daan R. Speth ◽  
Victoria J. Orphan
Keyword(s):  
De Novo ◽  
Alignment Score ◽  
Small Subset ◽  
Sequencing Technology ◽  
Large Protein ◽  
The Family ◽  
Complex Protein ◽  
Functionally Diverse ◽  
Score Matrix

AbstractRapid advances in sequencing technology have resulted in the availability of genomes from organisms across the tree of life. Accurately interpreting the function of proteins in these genomes is a major challenge, as annotation transfer based on homology frequently results in misannotation and error propagation. This challenge is especially pressing for organisms whose genomes are directly obtained from environmental samples, as interpretation of their physiology and ecology is often based solely on the genome sequence. For complex protein (super)families containing a large number of sequences, classification can be used to determine whether annotation transfer is appropriate, or whether experimental evidence for function is lacking. Here we present a novel computational approach for de novo classification of large protein (super)families, based on clustering an alignment score matrix obtained by aligning all sequences in the family to a small subset of the data. We evaluate our approach on the enolase family in the Structure Function Linkage Database.Availability and implementationASM-Clust is implemented in bash with helper scripts in perl. Scripts comprising ASM-Clust are available for download from https://github.com/dspeth/bioinfo_scripts/tree/master/ASM_clust/

scholarly journals Membrane transporters and folate homeostasis: intestinal absorption and transport into systemic compartments and tissues

2009 ◽  
Vol 11 ◽  
Author(s):  
Rongbao Zhao ◽  
Larry H. Matherly ◽  
I. David Goldman
Keyword(s):  
De Novo ◽  
Autosomal Recessive Disorder ◽  
Transport Systems ◽  
Loss Of Function ◽  
Folate Transport ◽  
Unique Role ◽  
The Family ◽  
Folate Transporters ◽  
Folate Homeostasis ◽  
Functionally Diverse

Members of the family of B9 vitamins are commonly known as folates. They are derived entirely from dietary sources and are key one-carbon donors required for de novo nucleotide and methionine synthesis. These highly hydrophilic molecules use several genetically distinct and functionally diverse transport systems to enter cells: the reduced folate carrier, the proton-coupled folate transporter and the folate receptors. Each plays a unique role in mediating folate transport across epithelia and into systemic tissues. The mechanism of intestinal folate absorption was recently uncovered, revealing the genetic basis for the autosomal recessive disorder hereditary folate malabsorption, which results from loss-of-function mutations in the proton-coupled folate transporter gene. It is therefore now possible to piece together how these folate transporters contribute, both individually and collectively, to folate homeostasis in humans. This review focuses on the physiological roles of the major folate transporters, with a brief consideration of their impact on the pharmacological activities of antifolates.

Review of The Self in the Family: A Classification of Personality, Criminality, and Psychopathology.

1997 ◽  
Vol 42 (11) ◽  
pp. 1042-1042
Author(s):  
Terri Gullickson
Keyword(s):  
The Self ◽  
The Family

Three new species, two new genera, and new family Biphragmosagittidae (Сhaetognatha) from Southwest Pacific Ocean

2011 ◽  
Vol 20 (1) ◽  
pp. 161-173
Author(s):  
A.P. Kassatkina
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characters ◽  
The Body ◽  
New Order ◽  
New Genera ◽  
New Family ◽  
The Family ◽  
Three New Species

Resuming published and own data, a revision of classification of Chaetognatha is presented. The family Sagittidae Claus & Grobben, 1905 is given a rank of subclass, Sagittiones, characterised, in particular, by the presence of two pairs of sac-like gelatinous structures or two pairs of fins. Besides the order Aphragmophora Tokioka, 1965, it contains the new order Biphragmosagittiformes ord. nov., which is a unique group of Chaetognatha with an unusual combination of morphological characters: the transverse muscles present in both the trunk and the tail sections of the body; the seminal vesicles simple, without internal complex compartments; the presence of two pairs of lateral fins. The only family assigned to the new order, Biphragmosagittidae fam. nov., contains two genera. Diagnoses of the two new genera, Biphragmosagitta gen. nov. (type species B. tarasovi sp. nov. and B. angusticephala sp. nov.) and Biphragmofastigata gen. nov. (type species B. fastigata sp. nov.), detailed descriptions and pictures of the three new species are presented.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1342
Author(s):  
Shaghayegh Mehravi ◽  
Gholam Ali Ranjbar ◽  
Ghader Mirzaghaderi ◽  
Anita Alice Severn-Ellis ◽  
Armin Scheben ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Snps ◽  
The Family ◽  
Double Digestion ◽  
Flanking Sequences ◽  
Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

scholarly journals Transcriptomic and Proteomic Analyses Reveal the Diversity of Venom Components from the Vaejovid Scorpion Serradigitus gertschi

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 359 ◽  
Author(s):  
Maria Romero-Gutiérrez ◽  
Carlos Santibáñez-López ◽  
Juana Jiménez-Vargas ◽  
Cesar Batista ◽  
Ernesto Ortiz ◽  
...  
Keyword(s):  
Serine Proteases ◽  
De Novo ◽  
Sequence Similarity ◽  
Scorpion Venom ◽  
Secretory Proteins ◽  
Host Defense Peptides ◽  
The Family ◽  
Pathogenesis Related ◽  
Molecular Masses

To understand the diversity of scorpion venom, RNA from venomous glands from a sawfinger scorpion, Serradigitus gertschi, of the family Vaejovidae, was extracted and used for transcriptomic analysis. A total of 84,835 transcripts were assembled after Illumina sequencing. From those, 119 transcripts were annotated and found to putatively code for peptides or proteins that share sequence similarities with the previously reported venom components of other species. In accordance with sequence similarity, the transcripts were classified as potentially coding for 37 ion channel toxins; 17 host defense peptides; 28 enzymes, including phospholipases, hyaluronidases, metalloproteases, and serine proteases; nine protease inhibitor-like peptides; 10 peptides of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein superfamily; seven La1-like peptides; and 11 sequences classified as “other venom components”. A mass fingerprint performed by mass spectrometry identified 204 components with molecular masses varying from 444.26 Da to 12,432.80 Da, plus several higher molecular weight proteins whose precise masses were not determined. The LC-MS/MS analysis of a tryptic digestion of the soluble venom resulted in the de novo determination of 16,840 peptide sequences, 24 of which matched sequences predicted from the translated transcriptome. The database presented here increases our general knowledge of the biodiversity of venom components from neglected non-buthid scorpions.

A comparison of methodological approaches to the subfamilial classification of the Naididae (Oligochaeta)

1987 ◽  
Vol 65 (3) ◽  
pp. 691-707 ◽  
Author(s):  
A. F. L. Nemec ◽  
R. O. Brinkhurst
Keyword(s):  
Data Matrix ◽  
Jaccard Coefficient ◽  
Data Set ◽  
Parsimony Method ◽  
Fit Statistics ◽  
Reconstruction Methods ◽  
Linkage Methods ◽  
The Family ◽  
First Time

A data matrix of 23 generic or subgeneric taxa versus 24 characters and a shorter matrix of 15 characters were analyzed by means of ordination, cluster analyses, parsimony, and compatibility methods (the last two of which are phylogenetic tree reconstruction methods) and the results were compared inter alia and with traditional methods. Various measures of fit for evaluating the parsimony methods were employed. There were few compatible characters in the data set, and much homoplasy, but most analyses separated a group based on Stylaria from the rest of the family, which could then be separated into four groups, recognized here for the first time as tribes (Naidini, Derini, Pristinini, and Chaetogastrini). There was less consistency of results within these groups. Modern methods produced results that do not conflict with traditional groupings. The Jaccard coefficient minimizes the significance of symplesiomorphy and complete linkage avoids chaining effects and corresponds to actual similarities, unlike single or average linkage methods, respectively. Ordination complements cluster analysis. The Wagner parsimony method was superior to the less flexible Camin–Sokal approach and produced better measure of fit statistics. All of the aforementioned methods contain areas susceptible to subjective decisions but, nevertheless, they lead to a complete disclosure of both the methods used and the assumptions made, and facilitate objective hypothesis testing rather than the presentation of conflicting phylogenies based on the different, undisclosed premises of manual approaches.

scholarly journals De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures

2007 ◽  
Vol 23 (11) ◽  
pp. 1321-1330 ◽  
Author(s):  
Kwang Loong Stanley Ng ◽  
Santosh K. Mishra
Keyword(s):  
De Novo ◽  
Svm Classification

A revision of the subfamily Haplorchinae Looss, 1899 (Trematoda: Heterophyidae): I. The Haplorchis group

Parasitology ◽  
1964 ◽  
Vol 54 (4) ◽  
pp. 601-676 ◽  
Author(s):  
J. C. Pearson
Keyword(s):  
Life History ◽  
Ventral Sucker ◽  
Genital Pore ◽  
History Data ◽  
Life History Data ◽  
The Family ◽  
Excretory Bladder

Earlier schemes of classification of the family Heterophyidae have been based in large part on such features as shape of body, presence of oral spines, number and position of testes, and distribution of vitellaria (Witenberg, 1929; Ciurea, 1933; Mueller & Van Cleave, 1932). Price (1940a) was the first to make extensive use of features of the ventrogenital complex (ventral sucker, gonotyl, genital pore, terminal male duct) and excretory bladder, and produced the first reasonable classification of both the family Heterophyidae and the superfamily Opisthorchioidea. In despite of the obvious significance of the rationale of Price's approach, later authors (Morozov, 1952, 1955; Yamaguti, 1958) have largely ignored the ventrogenital complex and recently discovered life-history data, and have used much the same sorts of features as earlier authors.

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