Open reading frame identification software tools | Shotgun metagenomic sequencing data analysis
De novo sequencing and metagenomics sequencing studies generate unannotated sequences for which identification of open-reading frame (ORF) is a difficult task. Orf detection software tools use algorithms that scan sequences in search of start and stop codons to identify ORFs.
Assists in annotating complete or nearly complete bacterial and archaeal genomes. RAST is a fully-automated application provides high quality genome annotations for these genomes across the whole phylogenetic tree. It includes a user interface that allows registered users to make manual changes to their genomes before retrieving them. It was designed to extend annotations to as many protein-encoding genes in as many genomes as possible.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
A software tool for improving the results of conventional gene finders for prokaryotic genomes with regard to exact localization of the translation initiation site (TIS). At the current state TICO provides an interface for direct post processing of the predictions obtained from the widely used program GLIMMER. Although the underlying method is not based on any specific assumptions about characteristic sequence features of prokaryotic TIS the prediction rates of our tool are competitive on experimentally verified test data.
Provides sensitivity in identifying existing genes. Prodigal is a gene-finding program for microbial for genome annotation of either draft or finished microbial sequence. It was developed to predict translation initiation sites more accurately. This application also permits to minimize the number of false positive predictions. This method can be useful for automated microbial annotation pipelines.
Rapidly identifies open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.
Discovers the operons of any bacterial or archaeal genome sequence. Operon-mapper is composed of three steps: (1) data acquisition, (2) sequence investigation, and (3) construction of the results. It only requires the genomic sequences of bacterial and archaebacterial to make its prediction. This tool builds useful and relevant information that is common to most bacterial genome annotation projects.
Allows users to determine putative open reading frames based on tandem mass spectrometry (MS/MS) ion search results of a virtual protein database. Virtual protein merger is a software that considers peptides associated to a virtual protein in a same translation frame. Then, the program computes the probable position of the corresponding open reading frame by searching for flanking start and end codons while authorizing users to define a minimum threshold score for accepting a peptide match.
Enables microbiologists to work with and curate draft and completed genomes. GAMOLA2 allows automated annotation of draft and completed microbial genomes by assembling a wide array of different analyses. The software represents a wrapper to bring together a wide range of specialized individual software tools. The use of a customized version of the Artemis Java application ensures platform independence for subsequent curation and analyses.
Transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU detects open reading frames (ORFs) present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. It greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference.
Identifies protein-coding regions in genomic bacterial data. FramePlot offers a web application which can compute third-letter G+C content and detect the totality of open reading frames (ORFs) starting with a pre-defined codon in the sequence, for lastly generating its corresponding plots. The application contains options allowing users to set the image width or the step size. The results obtained can then be confronted to the GenBank database.
Provides a platform gathering ten sequence analysis. SeqCalc is divided into three sections: (i) "nucleotide calc" permits to compute codon statistics, annealing temperature or sequence, and includes some convertors and an ORF finder; (ii) "protein calc" authorizes to calculate iso-electric point and protein properties as well as to extract protein secondary structures and ;(iii) the "common calc" runs analysis on both protein and nucleotide sequences.
Offers a library dealing with Saccharomyces cerevisiae open reading frame (ORFs). C-SWAT is a software able to perform a genome engineering at 3’ ends of ORFs with the aim of assisting users in investigating yeast genome and proteome. The application allows the study of gene expression regulation as well as the exploration of genomic position effects. It can also be applied for high-throughput C-terminal protein tagging.
Allows users to detect candidate coding regions into transcript sequences. Transcoder is a standalone software that starts from either a FASTA or GFF file. The application also can scan and retain open reading frames (ORFs) for homology to known proteins by using a BlastP or a Pfam search and incorporate the results into the obtained selection. Predictions can then be visualized by using a genome browser such as IGV.
Views genes and predicts Open Reading Frames (ORFs) in one or a series of genomes. VGO is an easy-to-use genome browser that searches for sequences within genomes. It searches the translated genome for matches to mass spec peptides and for the longest oligonucleotide shared between a series of unaligned genomes. VGO also views genes and predicted ORFs in one or a series of genomes. Because VGO talks to VOCs (Viral Orthologous Clusters) database of genome sequences, it can be used to compare genomes.
Assists user in translation of DNA sequences. ORF search & Translator is a web server utility that can also search Open Reading Frames (ORF). Users can choose genetic code such as vertebrate or invertebrate mitochondrial, echinoderm mitochondrial, ascidian mitochondrial, ciliate macronuclear and dasycladacean, blepharisma nuclear code, eubacterial, or alternative ciliate macronuclear.
Provides an environment to execute various bioinformatics analyses, data management and graphical viewing. CLC Sequence Viewer allows multiple alignment of DNA, RNA, proteins and consensus sequence determination and management. Users can generate reverse complement, translate DNA to protein, open reading frame determination or process neighbor-joining and unweighted pair group method with arithmetic mean (UPGMA) phylogenies.
Searches open reading frames (ORFs) in the DNA sequence. Open Reading Frame Finder returns the range of each ORF, along with its protein translation. It uses ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP. This web version of the ORF finder is limited to the subrange of the query sequence up to 50 kb long, but the stand-alone version, doesn't have query sequence length limitation.
Serves to identify small open reading frames (sORFs) with 10 to 100 amino acids and with high-coding potential in all six frames of a given nucleotide sequence. SORF finder works with a set of 5 programs: (1) make_model.pl, (2) simulate.pl, (3) search_sORF.pl, (4) collect_homo.pl, and (5) examine_SP.pl. . This tool comprises a software package and a web application.