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https://www.readbyqxmd.com/read/28645150/gfapy-a-flexible-and-extensible-software-library-for-handling-sequence-graphs-in-python
#1
Giorgio Gonnella, Stefan Kurtz
Summary: GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Availability and Implementation: GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. Contact: gonnella@zbh.uni-hamburg.de. Supplementary information: Supplementary data are available at Bioinformatics online...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#2
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#3
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28630199/genome-wide-analysis-of-the-antimicrobial-peptides-in-python-bivittatus-and-characterization-of-cathelicidins-with-potent-antimicrobial-activity-and-low-cytotoxicity
#4
Dayeong Kim, Nagasundarapandian Soundrarajan, Juyeon Lee, Hye-Sun Cho, Minkyeung Choi, Se-Yeoun Cha, Byeongyong Ahn, Hyoim Jeon, Minh Thong Le, Hyuk Song, Jin-Hoi Kim, Chankyu Park
In this study, we sought to identify novel antimicrobial peptides (AMPs) in Python bivittatus through bioinformatic analyses of publicly available genome information and experimental validation. In our analysis of the python genome, we identified 29 AMP-related candidate sequences. Of these, we selected five cathelicidin-like sequences and subjected them to further in silico analyses. The results showed that these sequences likely have antimicrobial activity. The sequences were named Pb-CATH1-Pb-CATH5 according to their sequence similarity to previously reported snake cathelicidins...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28605539/runbng-a-software-package-for-bionano-genomic-analysis-on-the-command-line
#5
Yuxuan Yuan, Philipp E Bayer, HueyTyng Lee, David Edwards
Summary: We developed runBNG, an open-source software package which wraps BioNano genomic analysis tools into a single script that can be run on the command line. runBNG can complete analyses, including quality control of single molecule maps, optical map de novo assembly, comparisons between different optical maps, super-scaffolding and structural variation detection. Compared to existing software BioNano IrysView and the KSU scripts, the major advantages of runBNG are that the whole pipeline runs on one single platform and it has a high customizability ...
June 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582565/isambard-an-open-source-computational-environment-for-biomolecular-analysis-modelling-and-design
#6
Christopher W Wood, Jack W Heal, Andrew R Thomson, Gail J Bartlett, Amaurys A Ibarra, R Leo Brady, Richard B Sessions, Derek N Woolfson
Motivation: The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Results: Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico ...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582538/breakpoint-surveyor-a-pipeline-for-structural-variant-visualization
#7
Matthew A Wyczalkowski, Kristine M Wylie, Song Cao, Michael D McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C Wendl, Li Ding
Summary: BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-Seq expression into a single comprehensive figure. Availability: Source code and sample data freely available for download at https://github...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582485/compass-the-completely-arbitrary-sequence-simulator
#8
Andrew Low, Nicolas Rodrigue, Alex Wong
Summary: Simulated sequence alignments are frequently used to test bioinformatics tools, but current sequence simulators are limited to defined state spaces. Here, we present the COMPletely Arbitrary Sequence Simulator (COMPASS), which is able to simulate the evolution of absolutely any discrete state space along a tree, for any form of time-reversible model. Availability and Implementation: COMPASS is implemented in Python 2.7, and is freely available for all platforms with the Supplemetary Information, as well as at http://labs...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28582481/fungap-fungal-genome-annotation-pipeline-using-evidence-based-gene-model-evaluation
#9
Byoungnam Min, Igor V Grigoriev, In-Geol Choi
Motivation: Successful genome analysis depends on the quality of gene prediction. Although fungal genome sequencing and assembly have become trivial, its annotation procedure has not been standardized yet. Results: FunGAP predicts protein-coding genes in a fungal genome assembly. To attain high-quality gene models, this program runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575169/md-task-a-software-suite-for-analyzing-molecular-dynamics-trajectories
#10
David K Brown, David L Penkler, Olivier Sheik Amamuddy, Caroline Ross, Ali Rana Atilgan, Canan Atilgan, Özlem Tastan Bishop
Summary: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28572580/uropa-a-tool-for-universal-robust-peak-annotation
#11
Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28498885/proximate-a-database-of-mutant-protein-protein-complex-thermodynamics-and-kinetics
#12
Sherlyn Jemimah, K Yugandhar, M Michael Gromiha
Summary: We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data...
May 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472345/stopgap-a-database-for-systematic-target-opportunity-assessment-by-genetic-association-predictions
#13
Judong Shen, Kijoung Song, Andrew Slater, Enrico Ferrero, Matthew R Nelson
Summary: We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes...
May 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472272/modlamp-python-for-antimicrobial-peptides
#14
Alex T Müller, Gisela Gabernet, Jan A Hiss, Gisbert Schneider
Summary: We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification, and visual representation of peptide data. modlAMP offers functions for molecular descriptor calculation and the retrieval of amino acid sequences from public or local sequence databases, and provides instant access to precompiled data sets for machine learning. The package also contains methods for the analysis and representation of circular dichroism spectra...
May 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472230/omsim-a-simulator-for-optical-map-data
#15
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire genome. In turn, these optical maps can be used to validateor improve de novo genome assembly projects or to detect large-scale structural variation in genomes. Simulated optical map data can assist in the development and benchmarking of tools that operate on thosedata, such as alignment and assembly software...
May 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453684/mappi-dat-data-management-and-analysis-for-protein-protein-interaction-data-from-the-high-throughput-mappit-cell-microarray-platform
#16
Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens
Summary: Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#17
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449031/rnablueprint-flexible-multiple-target-nucleic-acid-sequence-design
#18
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L Hofacker, Sven Findeiß
Motivation: Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28431529/hirbin-high-resolution-identification-of-differentially-abundant-functions-in-metagenomes
#19
Tobias Österlund, Viktor Jonsson, Erik Kristiansson
BACKGROUND: Gene-centric analysis of metagenomics data provides information about the biochemical functions present in a microbiome under a certain condition. The ability to identify significant differences in functions between metagenomes is dependent on accurate classification and quantification of the sequence reads (binning). However, biological effects acting on specific functions may be overlooked if the classes are too general. METHODS: Here we introduce High-Resolution Binning (HirBin), a new method for gene-centric analysis of metagenomes...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28409116/prepare_taxa_charts-py-a-python-program-to-automate-generation-of-publication-ready-taxonomic-pie-chart-images-from-qiime
#20
Vijay Lakhujani, Chandan Badapanda
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names...
June 2017: Genomics Data
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