Resources
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PRESENTATIONS
APPLICATIONS and TOOLS
Optimized hybrid data structure
based on the ternary search trees
| Project Name: | Impact of functional polymorphisms influencing inflammation and oxidative stress on outcome and selection of treatment in chronic lymphocytic leukemia. |
| Project Number: | AZV 16-32339A (P03) |
| Authors: | Rostislav Hřivňák, Petr Gajdoš |
| Type: | standalone desktop application/libraries |
| Resource: |
The ZIP archive contains highly optimized hybrid data structure based on the ternary search trees and hash tables which can be used for indexing of genome data in form of k-mers obtained from genome in FASTA format. It also contains file parsers, utilities, suffix tree implementation, and test functions used for performance measurement. Source code is an attachment to Fast Hybrid Data Structure for a Large Alphabet K-Mers Indexing for Whole Genome Alignment article.
annotsv
svc
om-annotsv-svc:
Optical Mapping and AnnotSV Structural Variant Comparator
| Project Name: | Impact of functional polymorphisms influencing inflammation and oxidative stress on outcome and selection of treatment in chronic lymphocytic leukemia. |
| Project Number: | AZV 16-32339A (P03) |
| Authors: | Tomáš Novosád, Jakub Savara |
| Type: | standalone desktop application |
| Resource: |
A software tool for comparison of structural variants identified by optical mapping technology (Bionano Genomics) and long-read next-generation sequencing technologies i.e. 10xGenomics, Oxford Nanopore Technologies and Pacific Biosciences. Structural variants produced by long-read next-generation sequencing technologies are analyzed using AnnotSV software tool. The tool computes the distance variance between the Bionano and AnnotSV genomic coordinates for the beginning and end of individual SVs. Various types of filtering, such as overlapping gene filter, variant type filter or distance sum variance filter can be used. The tool is provided as CLI application and is platform independent.
CLL calculator:
Application for Risk Assessment of Patients with Chronic Lymphocytic Leukemia
| Project Name: | Impact of functional polymorphisms influencing inflammation and oxidative stress on outcome and selection of treatment in chronic lymphocytic leukemia. |
| Project Number: | AZV 16-32339A (P03) |
| Authors: | Gajdoš Petr, Běhálek Marek, Kriegová Eva, Schneiderová Petra |
| Type: | standalone desktop application, windows10 |
| Resource: | This resource is available after sign in. In case you have no credentials, send a request to the contact e-mail. |
This software tool is used to calculate statistically significant rules over the data collection. It is assumed that the input file will contain the binary values of the attributes (DNA snips) of individual patients obtained during the examination. The outcome is represented by an evaluation of the chances of occurrence of the disease / complication. The tool supports the deciding making process whether to start or change the course of treatment.
OLGEN Coverage Limit calculator
| Project Name: | Impact of functional polymorphisms influencing inflammation and oxidative stress on outcome and selection of treatment in chronic lymphocytic leukemia. |
| Project Number: | AZV 16-32339A (P03) |
| Authors: | Vašinek Michal, Novosád Tomáš, Petráčková Anna, Kriegová Eva |
| Type: | web application |
| Resource: |
The software allows to calculate the required coverage depth of the sequenced DNA segment to detect somatic mutations in the human genome. The software implements a newly designed probability model that calculates the required sequence coverage depth for a given n-percent somatic mutation and a defined error rate of measurement.
Periprosthetic Joint Infection Calculator
| Project Name: | Prediction for reoperation in patients with THA and TKA based on immunogenetic signature: development of risk calculator for routine clinical practice. |
| Project Number: | AZV 16-31852A |
| Authors: | Radvanský Martin, Kudělka Miloš, Kriegová Eva, Gallo Jiří |
| Type: | standalone desktop application, windows10 |
| Resource: | This resource is available after sign in. In case you have no credentials, send a request to the contact e-mail. |
The software is created for clinicians' needs as a support tool for deciding on the patient's condition based on the laboratory results. The tool can be used in the fields of medicine and bioinformatics with a focus on clinical testing.
Total Knee Arthroplasty Revision Occurrence Calculator
| Project Name: | Prediction for reoperation in patients with THA and TKA based on immunogenetic signature: development of risk calculator for routine clinical practice. |
| Project Number: | AZV 16-31852A |
| Authors: | Radvanský Martin, Kudělka Miloš, Kriegová Eva, Gallo Jiří |
| Type: | standalone desktop application, windows10 |
| Resource: | This resource is available after sign in. In case you have no credentials, send a request to the contact e-mail. |
The software is created for clinicians' needs to decide on the patient's condition and future TKA postoperative development based on clinical parameters and preoperative patient behavior. The tool can be used in the fields of medicine and bioinformatics with a focus on clinical testing.