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PolyPhred
Compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. PolyPhred is not a standalone application. PolyPhred's functions are integrated with the use of three other programs: Phred, Phrap, and Consed. PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
Consed
A program for viewing and editing assemblies prepared by the Phrap assembly program. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads.
PineSAP / Pine Alignment and SNP Identification Pipeline
Provides a high-throughput solution to single nucleotide polymorphism (SNP) prediction using multiple sequence alignments from re-sequencing data. This pipeline integrates a hybrid of customized scripting, existing utilities and machine learning in order to increase the speed and accuracy of SNP calls. The implementation of this pipeline results in significantly improved multiple sequence alignments and SNP identifications when compared with existing solutions. The use of machine learning in the SNP identifications extends the pipeline's application to any eukaryotic species where full genome sequence information is unavailable.
AutoCSA / Automatic Comparative Sequence Analysis
A mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. AutoCSA is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity. AutoCSA is split into three main components, pre-processing of the trace file, variant detection and a post-processing stage to remove false positives. It has specifically been written with high throughput environments in mind, so it is easy to automate the analysis of large amounts of data with little manual intervention.
GeneScreen
A desktop program that analyses capillary electropherograms and compares their sequences with a known reference for identification of mutations. The detected sequence variants are then made available for rapid assessment and annotation via a graphical user interface, allowing chosen variants to be exported for reporting and archiving. The program was validated using more than 16,000 diagnostic laboratory sequence traces. Using GeneScreen, a single user requires only a few minutes to identify rare mutations in hundreds of sequence traces, with comparable sensitivity to expensive commercial products.
ODS / Online Diagnostic System
Analyses the Sanger sequencing data and provides an easy-to-use one-step solution for genetic testing data analysis. ODS seamlessly integrates base calling, single nucleotide variation (SNV) identification, and SNV annotation into one single platform. It also allows laboratorians to manually inspect the quality of the identified SNVs in the final report. ODS can significantly reduce the data analysis time therefore allows Sanger sequencing-based genetic testing to be finished in a timely manner.
VarDetect
Detects single nucleotide polymorphisms (SNPs) efficiently from fluorescence based chromatogram data and interprets fluorescence based chromatograms and efficiently detect the corresponding nucleotide variations in an automatic fashion. In this framework, three main heuristic procedures are employed: i) partitioning and re-sampling (PnR) algorithm that may be used to base-call the bases with ambiguous signal, ii) calculation of the observed signal intensity ratio and vicinity intensity ratio, and iii) conversion of the chromatogram inputs to numeric code. VarDetect supersedes existing automatic SNP detection tools through utilization of rules which account for the common sequence reading artifacts, combined with pre-calculated peak content base ratios.
DiSNPindel
A computation tool to improve the detection of intra-individual SNPs and InDels in direct amplicon sequencing of a diploid. Neither reference sequence nor additional sample was required. Using two real datasets, we demonstrated the usefulness of DiSNPindel in its ability to improve largely the true SNP and InDel discovery rates and reduce largely the missed and false positive rates as compared with existing detection methods. DiSNPindel provides an efficient tool for intra-individual SNP and InDel detection in diploid amplicon sequencing. It will also be useful for identification of DNA variations in expressed sequence tag (EST) re-sequencing.
Phrap
Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses a banded version of the Smith-Waterman-Gotoh algorithm to do pairwise comparisons of the sequences. It compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet criteria, tries to extend the alignment if a match of the designated word size is found and then scores it. The software uses quality values produced by the PHRED basecaller. Cross match/Swat is included in the PHRAP package.
Indigo
Discovers mutations generated by genome editing tools such as CRISPR/Cas9, ZNFs or TALENs. Indigo is a rapid single nucleotide polymorphism (SNP) & Insertion-Deletion (InDel) discovery method in Chromatogram traces obtained from Sanger sequencing of polymerase chain reaction (PCR) products. It can separate a mutated and wildtype allele and aligns both alleles against a reference sequence or wildtype chromatogram. Indigo can be run online as a web application or compiled from source.
PeakHeights
A tool for detecting germline microsatellite instability in mismatch repair-deficient subjects. PeakHeights can quickly and simply determine a parameter called the gMSI ratio, based on alterations in electropherogram profile due to microsatellite instability. This can be used as a high-throughput screen in patients whose clinical picture suggests the possibility of biallelic mutations in one of the mismatch repair genes such as PMS2 or MSH2. PeakHeights is also a flexible and powerful general tool for determining signal intensities of selected peaks within ABI electropherograms and exporting them into spreadsheets for easy manipulation. Large batches of samples can be processed at once.
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