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The ORF Finder (Open Reading Frame Finder) [16] is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes.
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-coding sequences: Fungi, Prokaryotes, Metazoa, Protist, Plants [41] [42] PHANOTATE: A tool to annotate phage genomes. Phages [43] SplicePredictor
OrthoFinder is a command-line software tool for comparative genomics. [ 1 ] [ 2 ] OrthoFinder determines the correspondence between genes in different organisms (also known as orthology analysis). This correspondence provides a framework for understanding the evolution of life on Earth, and enables the extrapolation and transfer of biological ...
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper Improved microbial identification with GLIMMER. [4] This paper [4] provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER.
Online toolboxes, such as FaBox [22] or the FASTX-Toolkit within Galaxy servers, are also available. [23] These can be used to segregate sequence headers/identifiers, rename them, shorten them, or extract sequences of interest from large FASTA files based on a list of wanted identifiers (among other available functions).
An upstream open reading frame (uORF) is an open reading frame (ORF) within the 5' untranslated region (5'UTR) of an mRNA. uORFs can regulate eukaryotic gene expression. [1] [2] Translation of the uORF typically inhibits downstream expression of the primary ORF. However, in some genes such as yeast GCN4, translation of specific uORFs may ...
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 ...