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REAL is an efficient, accurate, and sensitive tool for aligning short reads obtained from next-generation sequencing. The programme can handle an enormous amount of single-end reads generated by the next-generation Illumina/Solexa Genome Analyzer. cREAL is a simple extension of REAL for aligning short reads obtained from next-generation ...
A combination of tools is employed: PALMapper (reads alignment), mTiM and mGene (inference of new transcripts). Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online ...
This is a list of free and open-source software (FOSS) packages, computer software licensed under free software licenses and open-source licenses.Software that fits the Free Software Definition may be more appropriately called free software; the GNU project in particular objects to their works being referred to as open-source. [1]
A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics ...
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
The 5 prime portion of the RC probe contains the reverse complement sequence of the desired target specific primer sequence. In RC-PCR, no target specific primers are present in the reaction mixture. Instead target specific primers are formed as the reaction proceeds. A typical reaction employing the approach requires four oligonucleotides. The ...
Rigi is an interactive graph editor tool for software reverse engineering using the white box method, i.e. necessitating source code, [1] [2]: 88 thus it is mainly aimed at program comprehension. [ 3 ] : 99 Rigi is distributed by its main author, Hausi A. Müller and the Rigi research group at the University of Victoria .
These types of false-positive variants are filtered out by the duplex sequencing method since mutations need to be accurately matched in both strands of DNA to be validated as true mutations. Duplex sequencing can theoretically detect mutations with frequencies as low as 10 −8 compared to the 10 −2 rate of standard NGS methods. [1] [2] [10]