Local BLAST database v1

protocols.io ◽  
2016 ◽  
Author(s):  
Rekha Seshadri
Keyword(s):  
Blast Database

scholarly journals PSV-37 Reemergence of cyathostomins species demonstrates anthelmintic resistance following drug administration in horses

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 335-335
Author(s):  
Alexa C Johnson ◽  
Amy S Biddle
Keyword(s):  
Anthelmintic Resistance ◽  
Macrocyclic Lactones ◽  
Number Of Species ◽  
Molecular Approaches ◽  
Pyrantel Pamoate ◽  
Drug Classes ◽  
Blast Database ◽  
Resistance Patterns ◽  
Near Future ◽  
Ncbi Blast

Abstract Arbitrary administration of anthelmintics to control equine gastrointestinal worms has led to increased resistance to the three broad-spectrum drug classes; benzimidazoles, tetrahydropyrimidines, and macrocyclic lactones. With little promise of new drug classes to target cyathostomins being introduced to the market in the near future, anthelmintic drugs must be administered judiciously to prevent complete anthelmintic parasite resistance. The objective of this study is to determine the reemergence rate of cyathostomins following three commercial horse dewormers during summer. Nine horses housed at two locations were enrolled to the study and was repeated June–September through 2017–2019. Horses were removed from the study if sequencing failed due to low egg recovery for more than 50% of the timepoints. Ivermectin (macrocyclic lactones; n = 6), Moxidectin (macrocyclic lactones; n = 8) and Strongid (pyrantel pamoate; n = 8) were administered to horses and fecal samples were collected every 14d for 98d. Samples were tested using fecal egg counts with a modified McMaster technique and 18S rRNA profiling of the V5.8 and ITS1 regions. Sequences were clustered and taxonomy was assigned against a custom NCBI Blast+ database with the aligned sequences of 19 cyathostomins. Data were analyzed using presence/absence methods in R studio. Treatment and Day significantly impacted the average number of species present (P < 0.001). Moxidectin had the lowest number of species present followed by Strongid then Ivermectin (7.14, 10.17, 11.09, respectively). Equine shedder status had no effect on the average number of species present (P > 0.05). Six species, CO. labiatus, CS. catinatum, CY. auriculatus, CY. elongatus, CT. goldi and CT. longibursatus, showed resistance to the three treatments (P > 0.05). Moxidectin was the most effective at eradicating cyathostomins infestations (P < 0.05). Identifying resistance patterns at the species level will enable mechanistic molecular approaches to determine anthelmintic resistance in cyathostomins.

scholarly journals Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa

2014 ◽  
Vol 80 (17) ◽  
pp. 5515-5521 ◽  
Author(s):  
Suzanne L. Ishaq ◽  
André-Denis G. Wright
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Hypervariable Regions ◽  
Blast Database ◽  
Primer Sets ◽  
18S Rrna Genes ◽  
Ciliate Protozoa

ABSTRACTFour new primers and one published primer were used to PCR amplify hypervariable regions within the protozoal 18S rRNA gene to determine which primer pair provided the best identification and statistical analysis. PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29. The protozoal diversity of rumen contents from moose in Alaska was assessed. In the present study, primer set 1, P-SSU-316F and GIC758R (amplicon of 482 bases), gave the best representation of diversity using BLAST classification, and the set amplifiedEntodinium simplexandOstracodiniumspp., which were not amplified by the other two primer sets. Primer set 2, GIC1080F and GIC1578R (amplicon of 498 bases), had similar BLAST results and a slightly higher percentage of sequences that were identified with a higher sequence identity. Primer sets 1 and 2 are recommended for use in ruminants. However, primer set 1 may be inadequate to determine protozoal diversity in nonruminants. The amplicons created by primer set 1 were indistinguishable for certain species within the generaBandia,Blepharocorys,Polycosta, andTetratoxumand betweenHemiprorodon gymnoprosthiumandProrodonopsiscoli, none of which are normally found in the rumen.

scholarly journals AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Abhijeet Singh ◽  
Bettina Müller ◽  
Hans-Henrik Fuxelius ◽  
Anna Schnürer
Keyword(s):  
Carbon Fixation ◽  
Sequence Data ◽  
Gene Encoding ◽  
Formyltetrahydrofolate Synthetase ◽  
Protein Levels ◽  
Acetogenic Bacteria ◽  
Blast Database ◽  
Key Enzyme ◽  
Chemolithoautotrophic Bacteria ◽  
Taxonomic Studies

Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

scholarly journals Co-Occurrence of Viruses, Plant Pathogens, and Symbionts in an Underexplored Hemipteran Clade

2021 ◽  
Vol 11 ◽  
Author(s):  
McKinlee M. Salazar ◽  
Mônica T. Pupo ◽  
Amanda M. V. Brown
Keyword(s):  
Plant Pathogen ◽  
Plant Pathogens ◽  
Plant Viruses ◽  
Metagenomic Sequencing ◽  
Base Pairs ◽  
Shotgun Metagenomic Sequencing ◽  
Data Clusters ◽  
Blast Database ◽  
Insect Symbionts ◽  
Plant Pathogen Interactions

Interactions between insect symbionts and plant pathogens are dynamic and complex, sometimes involving direct antagonism or synergy and sometimes involving ecological and evolutionary leaps, as insect symbionts transmit through plant tissues or plant pathogens transition to become insect symbionts. Hemipterans such as aphids, whiteflies, psyllids, leafhoppers, and planthoppers are well-studied plant pests that host diverse symbionts and vector plant pathogens. The related hemipteran treehoppers (family Membracidae) are less well-studied but offer a potentially new and diverse array of symbionts and plant pathogenic interactions through their distinct woody plant hosts and ecological interactions with diverse tending hymenopteran taxa. To explore membracid symbiont–pathogen diversity and co-occurrence, this study performed shotgun metagenomic sequencing on 20 samples (16 species) of treehopper, and characterized putative symbionts and pathogens using a combination of rapid blast database searches and phylogenetic analysis of assembled scaffolds and correlation analysis. Among the 8.7 billion base pairs of scaffolds assembled were matches to 9 potential plant pathogens, 12 potential primary and secondary insect endosymbionts, numerous bacteriophages, and other viruses, entomopathogens, and fungi. Notable discoveries include a divergent Brenneria plant pathogen-like organism, several bee-like Bombella and Asaia strains, novel strains of Arsenophonus-like and Sodalis-like symbionts, Ralstonia sp. and Ralstonia-type phages, Serratia sp., and APSE-type phages and bracoviruses. There were several short Phytoplasma and Spiroplasma matches, but there was no indication of plant viruses in these data. Clusters of positively correlated microbes such as yeast-like symbionts and Ralstonia, viruses and Serratia, and APSE phage with parasitoid-type bracoviruses suggest directions for future analyses. Together, results indicate membracids offer a rich palette for future study of symbiont–plant pathogen interactions.

scholarly journals An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

2019 ◽  
Author(s):  
Prashant S. Hosmani ◽  
Mirella Flores-Gonzalez ◽  
Henri van de Geest ◽  
Florian Maumus ◽  
Linda V. Bakker ◽  
...  
Keyword(s):  
Single Molecule ◽  
Reference Genome ◽  
De Novo ◽  
Proximity Ligation ◽  
Contact Maps ◽  
Long Reads ◽  
Blast Database ◽  
Optical Maps ◽  
Almost All ◽  
454 Sequences

AbstractThe original Heinz 1706 reference genome was produced by a large team of scientists from across the globe from a variety of input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here the latest tomato reference genome (SL4.0) assembled de novo from PacBio long reads and scaffolded using Hi-C contact maps. The assembly was validated using Bionano optical maps and 10X linked-read sequences. This assembly is highly contiguous with fewer gaps compared to previous genome builds and almost all scaffolds have been anchored and oriented to the 12 tomato chromosomes. We have found more repeats compared to the previous versions and one of the largest repeat classes identified are the LTR retrotransposons. We also describe updates to the reference genome and annotation since the last publication. The corresponding ITAG4.0 annotation has 4,794 novel genes along with 29,281 genes preserved from ITAG2.4. Most of the updated genes have extensions in the 5’ and 3’ UTRs resulting in doubling of annotated UTRs per gene. The genome and annotation can be accessed using SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse genome browser and FTP available at https://solgenomics.net.

scholarly journals Gene expression profile in rat pancreatic islet and RINm5F cells

2005 ◽  
Vol 35 (1) ◽  
pp. 1-12 ◽  
Author(s):  
H Wang ◽  
Y Horikawa ◽  
L Jin ◽  
T Narita ◽  
S Yamada ◽  
...  
Keyword(s):  
Pancreatic Islet ◽  
Expression Profile ◽  
Large Scale ◽  
Expressed Sequence Tag ◽  
Homology Search ◽  
Cdna Libraries ◽  
Rinm5f Cells ◽  
Disease States ◽  
Blast Database ◽  
Rat Pancreatic Islet

To clarify tissue-specificity of pancreatic β cells, comparison of mRNA expression in various conditions of the tissue of multiple organisms is important. Although the developed methodologies for mRNA monitoring such as microarray, rely on the growth of dbEST (database of expressed sequence tag), a large number of unknown genes in the genome, especially in the rat, have not been shown to be expressed. In this study, we have established the first database of ESTs from rat pancreatic islet and RINm5F cells. Two cDNA libraries were constructed using mRNAs from rat pancreatic islet and RINm5F cells to cover a wider spectrum of expressed genes. Over 40 000 clones were randomly selected from the two libraries and partially sequenced. The sequences obtained were subjected to BLAST database analyses. This large-scale sequencing generated 40 710 3′-ESTs. Clustering analysis and homology search of nucleotide and peptide databases using both 3′- and 5′-ESTs revealed 10 406 non-redundant transcripts representing 4078 known genes or homologs and 6328 unknown genes. To confirm actual expression, the unknown sequences were further subjected to dbEST search, resulting in the identification of 5432 significant matches to those from other sources. Interestingly, of the remaining sequences showing no match, 779 were found to be encoded by exon–intron organization in the corresponding genomic sequences, suggesting that these are newly found as actually expressed in this study. Since many genes are up- or down-regulated in differing conditions, applications of the expression profile should facilitate identification of the genes involved in cell-specific functions in normal and disease states.

Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1013-1024 ◽  
Author(s):  
J Murray ◽  
J Larsen ◽  
T E Michaels ◽  
A Schaafsma ◽  
C E Vallejos ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Sulfur Metabolism ◽  
Branched Chain Amino Acid ◽  
Vacuolar Sorting Receptor ◽  
Blast Database ◽  
Early Nodulin ◽  
Vacuolar Sorting ◽  
Sorting Receptor ◽  
Branched Chain ◽  
Simple Sequence

A set of 79 previously mapped bean (Phaseolus vulgaris) genomic (Bng) clones were partially sequenced. BLAST database searches detected homologies between 59 of these clones and genes from a variety of plants, especially Arabidopsis thaliana. Some matches in the database to the Bng clones included a putative P-glycoprotein – ABC transporter from Arabidopsis, an early nodulin-binding protein (ENBP1) from Medicago truncatula, a lon-protease protein from spinach, a branched-chain amino-acid aminotransferase from Arabidopis, and a vacuolar sorting receptor (BP-80) from Pisum sativum. Additional matches were found for genes involved in isoprenoid biosynthesis, sulfur metabolism, proline biosynthesis, and floral development. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs). Polymorphisms were detected for six of the STSs.Key words: CAPS, SSR, molecular markers, gene identification.

scholarly journals Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads

2018 ◽  
Author(s):  
Grzegorz M Boratyn ◽  
Jean Thierry-Mieg ◽  
Danielle Thierry-Mieg ◽  
Ben Busby ◽  
Thomas L Madden
Keyword(s):  
Data Sets ◽  
Rna Seq ◽  
Seed Selection ◽  
Sequencing Technologies ◽  
Dna And Rna ◽  
Spliced Alignment ◽  
Long Reads ◽  
Wide Range ◽  
Blast Database ◽  
Innovative Techniques

ABSTRACTNext-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, especially with long reads. We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline. It uses innovative techniques that include the optimization of a spliced alignment score and selective masking during seed selection. We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its ability to discover introns on real RNA-seq data sets from PacBio, Roche and Illumina runs, and on six benchmarks, and compare it to other popular aligners. Additionally, we look at alignments of human idealized RefSeq mRNA sequences perfectly matching the genome. We show that Magic-BLAST is the best at intron discovery over a wide range of conditions and the best at mapping reads longer than 250 bases, from any platform. It is versatile and robust to high levels of mismatches or extreme base composition, and reasonably fast. It can align reads to a BLAST database or a FASTA file. It can accept a FASTQ file as input or automatically retrieve an accession from the SRA repository at the NCBI.

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