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  2. TRANSFAC - Wikipedia

    en.wikipedia.org/wiki/TRANSFAC

    Another application is to retrieve all TFs that regulate a given (set of) gene(s). In the context of systems-biological studies, the TF-target gene relations documented in TRANSFAC were used to construct and analyze transcription regulatory networks. [14] [15] By far the most frequent use of TRANSFAC is the computational prediction of potential ...

  3. List of gene prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_gene_prediction...

    Neural network promoter prediction: Prokaryotes, Eukaryotes [38] NNSPLICE: Neural network splice site prediction: Drosophila, Human [39] ORFfinder: Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non ...

  4. List of RNA structure prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_RNA_structure...

    Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that that the automated ...

  5. 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 ...

  6. Transcription factor - Wikipedia

    en.wikipedia.org/wiki/Transcription_factor

    Other transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA adjacent to regulated genes. These transcription factors are critical to making sure that genes are expressed in the right cell at the right time and in the right amount, depending on the changing requirements of the organism.

  7. EMBOSS - Wikipedia

    en.wikipedia.org/wiki/EMBOSS

    EMBOSS is a free c software analysis package developed for the needs of the molecular biology and bioinformatics user community. [1] The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.

  8. Transcription factor binding site databases - Wikipedia

    en.wikipedia.org/wiki/Transcription_factor...

    a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database: website [8] hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database: website [9] HOCOMOCO: a comprehensive collection of human and mouse transcription factor binding sites ...

  9. ANNOVAR - Wikipedia

    en.wikipedia.org/wiki/ANNOVAR

    This process can be modulated transcription factors which can enhance or inhibit binding of RNApol II. If the variant disrupts a transcription factor binding site then transcription of the gene could be altered causing changes in gene expression level and/or protein production amount. This changes could cause phenotypic variations.

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