Search Results for "junctions"

WingSegment is a MATLAB app-designed tool employing a hybrid approach of computer vision and graph theory for precise insect wing image segmentation. WingSegment detects cells, junctions, Pterostigma, and venation patterns, measuring geometric features and generating Voronoi patterns. The tool utilizes region-growing, thinning, and Dijkstra's algorithms for boundary detection, junction identification, and vein path extraction. It provides histograms and box plots of geometric features, facilitating comprehensive wing analysis. ...

QuCAT stands for Quantum Circuit Analyzer Tool. This open source python library provides standard analysis tools for superconducting electronic circuits, built around Josephson junctions. QuCAT features an intuitive graphical or programmatical interface to create circuits, the ability to compute their Hamiltonian, and a set of complimentary functionalities such as calculating dissipation rates or visualizing current flows in the circuit. QuCAT currently supports quantization in the basis of normal modes.

Implemented code for the reanalysis of somatic APP retrotransposition originally claimed by Lee at el (Nature, 2018). Modules for two different analyses--detection of intra-exonic junctions (IEJs) and estimation of APP gencDNA fraction--are provided. A detailed description of our analysis is available in our bioRxiv paper (https://bit.ly/35Kgfbu). [ Basic usage ] • Detection of IEJs connecting APP exons java -jar somaticAPP.jar -D -b input.bam [optional_arguments] * Input data: PRJNA577966 * The input bam should be mapped to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping • Estimation of gencDNA fraction java -jar somaticAPP.jar -F -b input.bam -a BWA_PATH -s SAMTOOLS_PATH [optional_arguments] * Input data: PRJNA493258 * The input bam should be a human-genome-mapped (hg38), coordinate-sorted, and duplicate-marked file. ...

AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as well as many conventional array-types (e.g., Affymetrix, Illumina, Agilent). This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction/exon read or microarray files along with some simple descriptions of the conditions that you're analyzing. ...

INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.

SpliceJumper is classification based splicing junction calling tool. For now, it accepts paired-end RNA-Seq reads as input, and calls out the junctions. Also do the alignment.

FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. ...

FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron). If you have Emboss, you can genarate a graphic with option -graph 1.

...It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count “links” between two exons. When there are overlapping exons, these are grouped into “exon groups” and unique portions of each exon in an exon group are identified which are used when assigning reads to an exon. The link counts ascertained from unique regions are normalized with the probability of observing such a link given the insert size distribution which is referred to as link coverage. ...

A package for mapping of spliced reads and unbiased detection of novel junctions from RNA-seq data.

HMMSplicer is an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.

The overall task of this project is to enable researchers to mine for the full gene sequences and all available gene features annotation (such as coding sequence start, exon/intron junctions, etc. in the publicl availale databases (such as genebank, ens