225:. However, less than 10% of the vertebrate mRNAs surveyed in an older study contained AUG codons in front of the major ORF. Interestingly, uORFs were found in two thirds of proto-oncogenes and related proteins. 64–75% of experimentally found translation initiation sites of sORFs are conserved in the genomes of human and mouse and may indicate that these elements have function. However, sORFs can often be found only in the minor forms of mRNAs and avoid selection; the high conservation of initiation sites may be connected with their location inside promoters of the relevant genes. This is characteristic of
298:
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.
242:
334:
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
260:
The ORF Finder (Open
Reading Frame Finder) 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. The
297:
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
273:
ORF Investigator is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their
140:, not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons. This more general definition can be useful in the context of
200:
of that region matches the frequency characteristic for the given organism's coding regions. Therefore, some authors say that an ORF should have a minimal length, e.g. 100 codons or 150 codons. By itself even a long open reading frame is not conclusive evidence for the presence of a
237:
Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames. The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations.
217:, usually < 100 codons in length, that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. 5’-UTR of about 50% of mammal mRNAs are known to contain one or several sORFs, also called
301:
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'
31:
335:
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.
913:
Schwartz AM, Putlyaeva LV, Covich M, Klepikova AV, Akulich KA, Vorontsov IE, et al. (October 2016). "Early B-cell factor 1 (EBF1) is critical for transcriptional control of SLAMF1 gene in human B cells".
245:
Example of a six-frame translation. The nucleotide sequence is shown in the middle with forward translations above and reverse translations below. Two possible open reading frames with the sequences are
274:
single letter amino acid code, and provides their locations in the sequence. The pairwise global alignment between the sequences makes it convenient to detect the different mutations, including
265:(BLAST) server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software (sequence analyser).
715:
Zanet J, Benrabah E, Li T, PĂ©lissier-Monier A, Chanut-Delalande H, Ronsin B, et al. (September 2015). "Pri sORF peptides induce selective proteasome-mediated protein processing".
366:
148:, where a start or stop codon may not be present in the obtained sequences. Such an ORF corresponds to parts of a gene rather than the complete gene.
318:
ORFik is a R-package in
Bioconductor for finding open reading frames and using Next generation sequencing technologies for justification of ORFs.
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465:
102:
site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete
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1032:
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98:(usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The
141:
1318:
1137:
Tjeldnes, HĂĄkon; Labun, Kornel; Torres
Cleuren, Yamila; Chyżyńska, Katarzyna; Świrski, Michał; Valen, Eivind (2021).
1292:- A multi-platform, java-based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence
1272:
261:
deduced amino acid sequence can be saved in various formats and searched against the sequence database using the
572:
Claverie JM, Poirot O, Lopez F (1997). "The difficulty of identifying genes in anonymous vertebrate sequences".
1013:
Dhar DV, Kumar MS (2012). "ORF Investigator: A New ORF finding tool combining
Pairwise Global Gene Alignment".
99:
952:
Pearson WR, Wood T, Zhang Z, Miller W (November 1997). "Comparison of DNA sequences with protein sequences".
1323:
358:
75:
173:
664:
Kute, Preeti Madhav; Soukarieh, Omar; Tjeldnes, Håkon; Trégouët, David-Alexandre; Valen, Eivind (2022).
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262:
83:
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864:"Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution"
303:
1111:
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646:
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Sieber P, Platzer M, Schuster S (March 2018). "The
Definition of Open Reading Frame Revisited".
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1305:- A webserver designed for ORF prediction and translation of a batch of EST or cDNA sequences
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followed by an open reading frame that is long enough to encode a typical protein, where the
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1063:"Cap-independent enhancement of translation by a plant potyvirus 5' nontranslated region"
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491:"Computational methods for the identification of genes in vertebrate genomic sequences"
165:
160:. Long ORFs are often used, along with other evidence, to initially identify candidate
1087:
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585:
431:
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One common use of open reading frames (ORFs) is as one piece of evidence to assist in
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are removed and exons are then joined together after transcription to yield the final
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650:
349:
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176:. For example, in a randomly generated DNA sequence with an equal percentage of each
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sequence. The presence of an ORF does not necessarily mean that the region is always
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35:
1286:- A free, fast and multi-platform desktop GUI tool for predicting and analyzing ORFs
1078:
981:
372:
161:
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are used for the gene alignment. The ORF Investigator is written in the portable
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39:
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Proceedings of the
National Academy of Sciences of the United States of America
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817:"Initiation codons within 5'-leaders of mRNAs as regulators of translation"
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642:
416:
1096:
995:
973:
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666:"Small Open Reading Frames, How to Find Them and Determine Their Function"
607:
Vakirlis, Nikolaos; Vance, Zoe; Duggan, Kate M.; McLysaght, Aoife (2022).
593:
516:
783:
79:
768:"uORFdb--a comprehensive literature database on eukaryotic uORF biology"
766:
Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A (January 2014).
289:, and is therefore available to users of all common operating systems.
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74:
will be "open" (the "reading", however, refers to the RNA produced by
30:
331:
226:
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1248:
1277:
1139:"ORFik: A comprehensive R toolkit for the analysis of translation"
185:
63:
862:
Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB (September 2012).
1280:- A web-based interactive tool for CCSB Human ORFeome Collection
916:
Biochimica et
Biophysica Acta (BBA) - Gene Regulatory Mechanisms
609:"De novo birth of functional microproteins in the human lineage"
283:
202:
125:
117:
113:
27:
DNA section marked with start and stop codon of different length
1289:
169:
91:
59:
66:. Usually, this is considered within a studied region of a
1190:"orfipy: a fast and flexible tool for extracting ORFs"
369:
ORF enabling complete ORF analysis of a BLAST report.
78:of the DNA and its subsequent interaction with the
34:Sample sequence showing three different possible
534:
532:
530:
528:
526:
545:Computational Genome Analysis: an introduction
1000:National Center for Biotechnology Information
390:
388:
8:
815:Geballe, A. P.; Morris, D. R. (April 1994).
136:of an ORF therefore only applies to spliced
128:for protein translation. In the context of
94:) and by definition cannot extend beyond a
71:
1223:
1205:
1164:
1154:
1112:"ORFik - Open reading frames in genomics"
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681:
632:
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188:. A simple gene prediction algorithm for
436:National Human Genome Research Institute
240:
29:
384:
1110:Kornel Labun, Haakon Tjeldnes (2018).
1061:Carrington JC, Freed DD (April 1990).
1188:Singh U, Wurtele ES (February 2021).
947:
945:
7:
213:Some short ORFs (sORFs), also named
70:DNA sequence, where only one of the
62:sequence between the start and stop
1273:Translation and Open Reading Frames
1015:Research Journal of Recent Sciences
460:. New York: W.W. Norton & Co.
106:would be made during translation.
25:
458:Microbiology: An Evolving Science
456:Slonczewski J, Foster JW (2009).
263:basic local alignment search tool
184:would be expected once every 21
1079:10.1128/JVI.64.4.1590-1597.1990
438:. National Institutes of Health
42:are highlighted in purple, and
1207:10.1093/bioinformatics/btab090
821:Trends in Biochemical Sciences
276:single nucleotide polymorphism
1:
586:10.1016/s0097-8485(96)00039-3
86:). Such an ORF may contain a
928:10.1016/j.bbagrm.2016.07.004
833:10.1016/0968-0004(94)90277-1
625:10.1016/j.celrep.2022.111808
326:orfipy is a tool written in
778:(Database issue): D60–D67.
280:Needleman–Wunsch algorithms
72:six possible reading frames
1340:
1156:10.1186/s12859-021-04254-w
18:Unidentified reading frame
683:10.3389/fgene.2021.796060
574:Computers & Chemistry
409:10.1016/j.tig.2017.12.009
215:Small open reading frames
100:transcription termination
90:(usually AUG in terms of
495:Human Molecular Genetics
58:are defined as spans of
881:10.1073/pnas.1207846109
737:10.1126/science.aac5677
430:Brody LC (2021-08-25).
359:sequence profiling tool
152:Biological significance
46:are highlighted in red.
1247:Singh U (2021-02-13),
1124:10.18129/B9.bioc.ORFik
1037:bioinformatics.ysu.edu
966:10.1006/geno.1997.4995
772:Nucleic Acids Research
247:
47:
670:Frontiers in Genetics
543:, Waterman M (2005).
508:10.1093/hmg/6.10.1735
244:
233:Six-frame translation
168:-coding regions in a
33:
489:Claverie JM (1997).
308:nontranslated region
287:programming language
1067:Journal of Virology
874:(37): E2424–E2432.
729:2015Sci...349.1356Z
723:(6254): 1356–1358.
304:untranslated region
229:gene, for example.
1319:Molecular genetics
1301:2015-12-22 at the
1143:BMC Bioinformatics
784:10.1093/nar/gkt952
397:Trends in Genetics
248:
209:Short ORFs (sORFs)
48:
1200:(18): 3019–3020.
922:(10): 1259–1268.
558:978-0-387-98785-9
467:978-0-393-97857-5
192:might look for a
132:, the start-stop
52:molecular biology
16:(Redirected from
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1267:External links
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1194:Bioinformatics
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1033:"OrfPredictor"
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827:(4): 159–164.
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1278:hORFeome V5.1
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1043:on 2015-12-22
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345:Coding region
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76:transcription
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1296:ORFPredictor
1254:, retrieved
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1197:
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1115:
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1045:. Retrieved
1041:the original
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1027:
1021:(11): 32–35.
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960:(1): 24–36.
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613:Cell Reports
612:
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451:
440:. Retrieved
435:
432:"Stop Codon"
425:
400:
396:
373:Micropeptide
325:
317:
307:
300:
296:
272:
269:Investigator
259:
246:highlighted.
236:
222:
218:
214:
212:
155:
146:metagenomics
130:gene finding
108:
55:
49:
40:Start codons
996:"ORFfinder"
539:Deonier R,
198:codon usage
194:start codon
190:prokaryotes
164:regions or
88:start codon
84:translation
68:prokaryotic
44:stop codons
1313:Categories
1284:ORF Marker
1256:2021-02-13
1149:(1): 336.
1047:2015-12-17
676:: 796060.
442:2021-08-25
379:References
182:stop-codon
178:nucleotide
174:translated
134:definition
111:eukaryotic
96:stop codon
1216:1367-4803
841:0968-0004
753:206639549
651:254966620
476:185042615
355:Sequerome
293:Predictor
1299:Archived
1234:33576786
1175:34147079
954:Genomics
936:27424222
900:22927429
802:24163100
745:26383956
702:35154250
643:36543139
634:10073203
541:Tavaré S
417:29366605
339:See also
251:Software
80:ribosome
1290:StarORF
1225:8479652
1166:8214792
1097:2319646
982:6413018
974:9403055
891:3443142
849:8016865
793:3964959
725:Bibcode
717:Science
693:8831751
594:9415985
517:9300666
122:introns
104:protein
1232:
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1088:249294
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649:
641:
631:
592:
555:
515:
474:
464:
415:
332:Cython
328:Python
322:orfipy
256:Finder
227:SLAMF1
186:codons
64:codons
978:S2CID
749:S2CID
647:S2CID
363:BLAST
314:ORFik
223:uORFs
138:mRNAs
118:exons
114:genes
1230:PMID
1212:ISSN
1171:PMID
1093:PMID
970:PMID
932:PMID
920:1859
896:PMID
845:PMID
837:ISSN
798:PMID
741:PMID
698:PMID
639:PMID
590:PMID
553:ISBN
513:PMID
472:OCLC
462:ISBN
413:PMID
367:NCBI
357:– A
284:Perl
203:gene
180:, a
144:and
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