scholarly journals amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool

2020 ◽  
Author(s):  
Travis J Lawrence ◽  
Dana L Carper ◽  
Margaret K Spangler ◽  
Alyssa A Carrell ◽  
Tomás A Rush ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Random Forest Classifier ◽  
Supplementary Information ◽  
Command Line ◽  
Prediction Tool ◽  
Promising Alternative ◽  
Peptide Prediction ◽  
User Friendly ◽  
Genome Scale ◽  
Scale Data

Abstract Summary Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data are not readily available. Here we present amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences using a random forest classifier. Availability and implementation amPEPpy is implemented in Python 3 and is freely available through GitHub (https://github.com/tlawrence3/amPEPpy). Supplementary information Supplementary data are available at Bioinformatics online.

Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants

2019 ◽  
Vol 35 (21) ◽  
pp. 4405-4407 ◽  
Author(s):  
Steven Monger ◽  
Michael Troup ◽  
Eddie Ip ◽  
Sally L Dunwoodie ◽  
Eleni Giannoulatou
Keyword(s):  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
In Silico Prediction ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Prediction Tools ◽  
Motif Prediction ◽  
Command Line Tool ◽  
Genome Scale

Abstract Motivation In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants. Results We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer. Availability and implementation Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals DamageProfiler: Fast damage pattern calculation for ancient DNA

2021 ◽  
Author(s):  
Judith Neukamm ◽  
Alexander Peltzer ◽  
Kay Nieselt
Keyword(s):  
Ancient Dna ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Central Importance ◽  
Command Line Interface ◽  
Analysis Pipeline ◽  
File Formats ◽  
Programming Knowledge ◽  
User Friendly

Abstract Motivation In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Results DamageProfiler is a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline. Availability All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler). Supplementary information Supplementary data are available at Bioinformatics online.

Newer Quinolones in the Treatment of Continuous Ambulatory Peritoneal Dialysis (CAPD) Related Infections

1990 ◽  
Vol 10 (2) ◽  
pp. 127-133 ◽  
Author(s):  
Paul Nikolaidis
Keyword(s):  
Peritoneal Dialysis ◽  
Continuous Ambulatory Peritoneal Dialysis ◽  
Adverse Reactions ◽  
Antimicrobial Agents ◽  
Hospital Staff ◽  
Gram Negative Bacteria ◽  
Promising Alternative ◽  
Gram Negative ◽  
Dosing Intervals ◽  
Good Oral Bioavailability

Newer fluoroquinolones such as ciprofloxacin, pefloxacin, ofloxacin, enoxacin, and fleroxacin are potent antimicrobial agents against many gram-negative bacteria, including Pseudomonas aeruginosa species and staphylococci-sensitive or resistant to methicillin. They are almost completely absorbed when given orally, reaching therapeutic plasma and dialysate concentrations, and their long half lives permit infrequent dosing intervals. Clinical studies on fluoroquinolones efficacy in continuous ambulatory peritoneal dialysis (CAPD) infections, although not extensive, demonstrate good results. They are well tolerated and the adverse reactions, consisting mainly of gastrointestinal disturbance, were uncommon, mild, and reversible. The fluoroquinolones offer a promising alternative to standard parenteral treatments in CAPD patients, while their good oral bioavailability makes them attractive and convenient for both patients and hospital staff. However, they must be used with caution until we have more information and gain further experience.

scholarly journals Ribo-ODDR: Oligo design pipeline for experiment-specific rRNA depletion in ribo-seq

2021 ◽  
Author(s):  
Ferhat Alkan ◽  
Joana Silva ◽  
Eric Pintó Barberà ◽  
William J Faller
Keyword(s):  
Ribosome Profiling ◽  
Supplementary Information ◽  
Experimental Conditions ◽  
Computational Framework ◽  
Rna Translation ◽  
Rrna Depletion ◽  
Selection For ◽  
Nucleotide Resolution ◽  
User Friendly ◽  
Oligo Design

Abstract Motivation Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of rRNA fragments. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, they may perform suboptimally in Ribo-seq. In order to overcome this, it is possible to use custom biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. Results Here, we first show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may be inefficient. Therefore we developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We experimentally show that Ribo-ODDR designed oligos outperform commercially available kits and lead to a significant increase in rRNA depletion in Ribo-seq. Availability Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR Supplementary information Supplementary data are available at Bioinformatics online.

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

2020 ◽  
Vol 36 (12) ◽  
pp. 3913-3915
Author(s):  
Hemi Luan ◽  
Xingen Jiang ◽  
Fenfen Ji ◽  
Zhangzhang Lan ◽  
Zongwei Cai ◽  
...  
Keyword(s):  
False Positive ◽  
Supplementary Information ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Metabolomics Data ◽  
Web Based ◽  
Tremendous Amount ◽  
Chromatographic Peaks ◽  
User Friendly

Abstract Motivation Liquid chromatography–mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement. Results To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies. Availability and implementation The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

2017 ◽  
Vol 8 ◽  
Author(s):  
Maria del Carmen Montero-Calasanz ◽  
Jan P. Meier-Kolthoff ◽  
Dao-Feng Zhang ◽  
Adnan Yaramis ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
Genome Scale ◽  
Data Call ◽  
Scale Data

scholarly journals CausalR: extracting mechanistic sense from genome scale data

2017 ◽  
Vol 33 (22) ◽  
pp. 3670-3672 ◽  
Author(s):  
Glyn Bradley ◽  
Steven J Barrett
Keyword(s):  
Genome Scale ◽  
Scale Data

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Santosh Kumar Upadhyay ◽  
Shailesh Sharma
Keyword(s):  
Operating Systems ◽  
High Throughput ◽  
Genomic Data ◽  
Prediction Tool ◽  
High Demand ◽  
Specific Target ◽  
Target Sites ◽  
High Throughput Detection ◽  
User Friendly

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

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