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.
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.
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.
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.
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.
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.
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.