scholarly journals Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

2016 ◽  
Author(s):  
Martin Šošić ◽  
Mile Šikić
Keyword(s):  
Exact Sequence ◽  
Open Source ◽  
Sequence Alignment ◽  
Test Data ◽  
Edit Distance ◽  
Source Code ◽  
Memory Usage ◽  
Pairwise Sequence Alignment ◽  
Link Type ◽  
Bioinformatics Tools

AbstractWe present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools.Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS.Contact:[email protected]

scholarly journals Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance

2017 ◽  
Vol 33 (9) ◽  
pp. 1394-1395 ◽  
Author(s):  
Martin Šošić ◽  
Mile Šikić
Keyword(s):  
Exact Sequence ◽  
Sequence Alignment ◽  
Edit Distance

scholarly journals Phigaro: high throughput prophage sequence annotation

2019 ◽  
Author(s):  
Elizaveta V. Starikova ◽  
Polina O. Tikhonova ◽  
Nikita A. Prianichnikov ◽  
Chris M. Rands ◽  
Evgeny M. Zdobnov ◽  
...  
Keyword(s):  
Test Data ◽  
High Throughput ◽  
Source Code ◽  
Sequence Annotation ◽  
Command Line ◽  
Link Type ◽  
Genome Maps ◽  
Transposon Insertion ◽  
Prophage Sequence

AbstractSummaryPhigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It provides putative taxonomic annotations that can distinguish tailed from non-tailed phages. It is applicable for mining prophage regions from large metagenomic datasets.AvailabilitySource code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

PETAL: a python tool for deep analysis of biological pathways

2020 ◽  
Author(s):  
Giuseppe Sgroi ◽  
Giulia Russo ◽  
Francesco Pappalardo
Keyword(s):  
Open Source ◽  
Signaling Pathways ◽  
Open Source Software ◽  
Kegg Pathway ◽  
Source Code ◽  
Therapeutic Targets ◽  
Biological Pathways ◽  
Long Distance ◽  
Bioinformatics Tools ◽  
Novel Therapeutic

Abstract Summary Although several bioinformatics tools have been developed to examine signaling pathways, little attention has been given to ever long-distance crosstalk mechanisms. Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth search. PETAL can contribute to discovering novel therapeutic targets or biomarkers that are potentially hidden and not considered in the network under study. Availability PETAL is a freely available open-source software. It runs on all platforms that support Python3. The user manual and source code are accessible from https://github.com/Pex2892/PETAL.

scholarly journals Matchathon: A guide to student-faculty connections in PhD programs

2020 ◽  
Author(s):  
Haley Amemiya ◽  
Zena Lapp ◽  
Cathy Smith ◽  
Margaret Durdan ◽  
Michelle DiMondo ◽  
...  
Keyword(s):  
Open Source ◽  
Source Code ◽  
Faculty Members ◽  
Retention Rates ◽  
Link Type ◽  
Shiny App ◽  
R Shiny ◽  
Web App ◽  
Phd Programs ◽  
The Web

AbstractRelevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

scholarly journals A RESTful API to serve BAM file with OAuth2 compatible authorization

2017 ◽  
Author(s):  
Julien Delafontaine ◽  
Sylvain Pradervand
Keyword(s):  
Open Source ◽  
Source Code ◽  
Variant Calling ◽  
Use Case ◽  
Web Interface ◽  
Sensitive Data ◽  
Link Type ◽  
Restful Service

AbstractSummaryBam-server is an open-source RESTful service to query slices of BAM files securely and manage their user accesses. A typical use case is the visualization of local read alignments in a web interface for variant calling diagnostic, without exposing sensitive data to unauthorized users through the network, and without moving the original - heavy - file. Bam-server follows the standard implementation of a protected resource server in the context of a typical token-based authorization protocol, supporting HMAC- and RSA-hashed signatures from an authorization server of choice.AvailabilityThe source code is available at https://github.com/chuv-ssrc/bam-server-scala, and a complete documentation can be found at http://bam-server-scala.readthedocs.io/en/latest/[email protected]

scholarly journals SurfStamp: 3D Printer Compatible Molecular Surface Representation

2020 ◽  
Author(s):  
Toshiyuki Oda
Keyword(s):  
Open Source ◽  
Source Code ◽  
3D Structure ◽  
Three Dimensional ◽  
Molecular Surface ◽  
3D Printer ◽  
3D Object ◽  
Link Type ◽  
Surface Models ◽  
Version 2.0

AbstractSurfStamp is an application that is used to generate textures for surface models of proteins. The textures contain information about surface residues and the information is drawn directly on the 3D object of the models. This approach is more intuitive than the labeling functions that most three-dimensional (3D) structure viewers use to show residue information. Therefore, the use of this application enables researchers, readers, or audiences to easily determine which residues are contributing the surface they are focusing on.AvailabilityThe application is provided under the open-source Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). The application and source code are available from https://github.com/yamule/SurfStamp-public/releases.

scholarly journals quasitools: A Collection of Tools for Viral Quasispecies Analysis

2019 ◽  
Author(s):  
Eric Marinier ◽  
Eric Enns ◽  
Camy Tran ◽  
Matthew Fogel ◽  
Cole Peters ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Distance ◽  
Open Source ◽  
Source Code ◽  
Viral Quasispecies ◽  
Consensus Sequences ◽  
Link Type ◽  
Version 2.0 ◽  
Amino Acid Variants

AbstractSummaryquasitools is a collection of newly-developed, open-source tools for analyzing viral quasispcies data. The application suite includes tools with the ability to create consensus sequences, call nucleotide, codon, and amino acid variants, calculate the complexity of a quasispecies, and measure the genetic distance between two similar quasispecies. These tools may be run independently or in user-created workflows.AvailabilityThe quasitools suite is a freely available application licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https://phac-nml.github.io/quasitools/[email protected]

scholarly journals DrawAlignR: An interactive tool for across run chromatogram alignment visualization

2020 ◽  
Author(s):  
Shubham Gupta ◽  
Justin Sing ◽  
Arshia Mahmoodi ◽  
Hannes Röst
Keyword(s):  
Open Source ◽  
Web Application ◽  
Source Code ◽  
Link Type ◽  
Interactive Tool ◽  
Cumulative Score ◽  
Alignment Algorithms ◽  
R Shiny ◽  
Software Platforms

AbstractMulti-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

scholarly journals CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer

2016 ◽  
Author(s):  
Malachi Griffith ◽  
Nicholas C Spies ◽  
Kilannin Krysiak ◽  
Adam C Coffman ◽  
Joshua F McMichael ◽  
...  
Keyword(s):  
Open Access ◽  
Precision Medicine ◽  
Open Source ◽  
Source Code ◽  
Supporting Evidence ◽  
Clinical Interpretation ◽  
Open Source Code ◽  
Link Type ◽  
Application Programming ◽  
Programming Interfaces

AbstractCIViC is an expert crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer (www.civicdb.org) describing the therapeutic, prognostic, and diagnostic relevance of inherited and somatic variants of all types. CIViC is committed to open source code, open access content, public application programming interfaces (APIs), and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

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