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  2. List of free and open-source software packages - Wikipedia

    en.wikipedia.org/wiki/List_of_free_and_open...

    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]

  3. List of sequence alignment software - Wikipedia

    en.wikipedia.org/wiki/List_of_sequence_alignment...

    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 ...

  4. List of RNA-Seq bioinformatics tools - Wikipedia

    en.wikipedia.org/wiki/List_of_RNA-Seq...

    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 ...

  5. List of open-source bioinformatics software - Wikipedia

    en.wikipedia.org/wiki/List_of_open-source...

    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 ...

  6. Dot plot (bioinformatics) - Wikipedia

    en.wikipedia.org/wiki/Dot_plot_(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.

  7. Rigi (software) - Wikipedia

    en.wikipedia.org/wiki/Rigi_(software)

    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 .

  8. Inverted repeat - Wikipedia

    en.wikipedia.org/wiki/Inverted_repeat

    An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. [1] The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, 5'---TTACGnnnnnn CGTAA---3' is an inverted repeat sequence.

  9. Reverse complement polymerase chain reaction - Wikipedia

    en.wikipedia.org/wiki/Reverse_Complement...

    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 ...