mutations, including single nucleotide polymorphism. Needleman–Wunsch algorithms are used for the gene alignment. The ORF Investigator is written in the portable Perl programming language, and is therefore available to users of all common operating systems. Predictor OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. ORF Predictor uses a combination of the two different ORF definitions mentioned above. It searches stretches starting with a start codon and ending at a stop codon. As an additional criterion, it searches for a stop codon in the 5' untranslated region (UTR or NTR, nontranslated region.) ORFik ORFik is a R-package in Bioconductor for finding open reading frames and using Next generation sequencing technologies for justification of ORFs. orfipy orfipy is a tool written in Python / Cython to extract ORFs in an extremely and fast and flexible manner. orfipy can work with plain or gzipped FASTA and FASTQ sequences, and provides several options to fine-tune ORF searches; these include specifying the start and stop codons, reporting partial ORFs, and using custom translation tables. The results can be saved in multiple formats, including the space-efficient BED format. orfipy is particularly faster for data containing multiple smaller FASTA sequences, such as de-novo transcriptome assemblies. See also Coding region Putative gene Sequerome – A sequence profiling tool that links each BLAST record to the NCBI ORF enabling complete ORF analysis of a BLAST report. Micropeptide References External links Translation and Open Reading Frames hORFeome V5.1 - A web-based interactive tool for CCSB Human ORFeome Collection ORF Marker - A free, fast and multi-platform desktop GUI tool for predicting and analyzing ORFs StarORF - A multi-platform, java-based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence ORFPredictor - A webserver designed for ORF prediction and translation of a batch of EST or cDNA sequences Molecular genetics Bioinformatics he:מסגרת קריאה#מסגרת