הומולוגיה של רצף
הערות שוליים

1 2 3 4  Koonin EV (2005). "Orthologs, paralogs, and evolutionary genomics". Annual Review of Genetics. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID 16285863.
↑  "Clustal FAQ #Symbols". Clustal. נבדק ב-8 בדצמבר 2014. {{cite web}}:  (עזרה)
1 2  Reeck GR, de Haën C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE,  et al. (באוגוסט 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi:10.1016/0092-8674(87)90322-9. PMID 3621342. {{cite journal}}:  (עזרה)
↑  Holman C (בינואר 2004). "Protein Similarity Score: A Simplified Version of the Blast Score as a Superior Alternative to Percent Identity for Claiming Genuses of Related Protein Sequences". Santa Clara High Technology Law Journal. 21 (1): 55. ISSN 0882-3383. {{cite journal}}:  (עזרה)
1 2  Fitch WM (ביוני 1970). "Distinguishing homologous from analogous proteins". Systematic Zoology. 19 (2): 99–113. doi:10.2307/2412448. JSTOR 2412448. PMID 5449325. Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism (for example, a and b hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of the gene reflects the history of the species (for example a hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact). {{cite journal}}:  (עזרה)
↑  Falciatore A, Merendino L, Barneche F, Ceol M, Meskauskiene R, Apel K, Rochaix JD (בינואר 2005). "The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas". Genes & Development. 19 (1): 176–87. doi:10.1101/gad.321305. PMC 540235. PMID 15630026. {{cite journal}}:  (עזרה)
↑  Fang G, Bhardwaj N, Robilotto R, Gerstein MB (במרץ 2010). "Getting started in gene orthology and functional analysis". PLOS Computational Biology. 6 (3): e1000703. Bibcode:2010PLSCB...6E0703F. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041. {{cite journal}}:  (עזרה)
↑  COGs: Clusters of Orthologous Groups of proteins

Tatusov RL, Koonin EV, Lipman DJ (באוקטובר 1997). "A genomic perspective on protein families". Science. 278 (5338): 631–7. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173. {{cite journal}}:  (עזרה)
↑  Correia K, Yu SM, Mahadevan R (בינואר 2019). "AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution". Database. 2019. doi:10.1093/database/baz022. PMC 6425859. PMID 30893420. {{cite journal}}:  (עזרה)
↑  eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M,  et al. (בינואר 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971. {{cite journal}}:  (עזרה)
↑  Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J,  et al. (בינואר 2014). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (Database issue): D231-9. doi:10.1093/nar/gkt1253. PMC 3964997. PMID 24297252. {{cite journal}}:  (עזרה)
↑  GreenPhylDB

Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (בינואר 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Research. 36 (Database issue): D991-8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457. {{cite journal}}:  (עזרה)
↑  Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C,  et al. (בינואר 2011). "GreenPhylDB v2.0: comparative and functional genomics in plants". Nucleic Acids Research. 39 (Database issue): D1095-102. doi:10.1093/nar/gkq811. PMC 3013755. PMID 20864446. {{cite journal}}:  (עזרה)
↑  Inparanoid: Eukaryotic Ortholog Groups

Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S,  et al. (בינואר 2010). "InParanoid 7: new algorithms and tools for eukaryotic orthology analysis". Nucleic Acids Research. 38 (Database issue): D196-203. doi:10.1093/nar/gkp931. PMC 2808972. PMID 19892828. {{cite journal}}:  (עזרה)
↑  Sonnhammer EL, Östlund G (בינואר 2015). "InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic". Nucleic Acids Research. 43 (Database issue): D234-9. doi:10.1093/nar/gku1203. PMC 4383983. PMID 25429972. {{cite journal}}:  (עזרה)
↑  Singh PP, Arora J, Isambert H (ביולי 2015). "Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes". PLOS Computational Biology. 11 (7): e1004394. Bibcode:2015PLSCB..11E4394S. doi:10.1371/journal.pcbi.1004394. PMC 4504502. PMID 26181593. {{cite journal}}:  (עזרה)
↑  "Vertebrate Ohnologs". ohnologs.curie.fr. נבדק ב-2018-10-12.
↑  Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D,  et al. (בינואר 2018). "The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces". Nucleic Acids Research. 46 (D1): D477–D485. doi:10.1093/nar/gkx1019. PMC 5753216. PMID 29106550. {{cite journal}}:  (עזרה)
↑  Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P,  et al. (בינואר 2017). "OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs". Nucleic Acids Research. 45 (D1): D744–D749. doi:10.1093/nar/gkw1119. PMC 5210582. PMID 27899580. {{cite journal}}:  (עזרה)
↑  Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD,  et al. (בינואר 2019). "OrthoInspector 3.0: open portal for comparative genomics". Nucleic Acids Research. 47 (D1): D411–D418. doi:10.1093/nar/gky1068. PMC 6323921. PMID 30380106. {{cite journal}}:  (עזרה)
↑  OrthologID

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (במרץ 2006). "OrthologID: automation of genome-scale ortholog identification within a parsimony framework". Bioinformatics. 22 (6): 699–707. doi:10.1093/bioinformatics/btk040. PMID 16410324. {{cite journal}}:  (עזרה)
↑  Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R (2009). "Gene orthology assessment with OrthologID".  In Posada D (ed.). Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. Humana Press. pp. 23–38. doi:10.1007/978-1-59745-251-9_2. ISBN 978-1-59745-251-9. PMID 19378138.
↑  OrthoMaM

Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (בנובמבר 2007). "OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics". BMC Evolutionary Biology. 7 (1): 241. Bibcode:2007BMCEE...7..241R. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139. {{cite journal}}:  (עזרה)
↑  Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V (ביולי 2014). "OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals". Molecular Biology and Evolution. 31 (7): 1923–8. doi:10.1093/molbev/msu132. PMID 24723423. {{cite journal}}:  (עזרה)
↑  Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJ, Ranwez V (באפריל 2019). "OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes". Molecular Biology and Evolution. 36 (4): 861–862. doi:10.1093/molbev/msz015. PMC 6445298. PMID 30698751. {{cite journal}}:  (עזרה)
↑  OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Chen F, Mackey AJ, Stoeckert CJ, Roos DS (בינואר 2006). "OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups". Nucleic Acids Research. 34 (Database issue): D363-8. doi:10.1093/nar/gkj123. PMC 1347485. PMID 16381887. {{cite journal}}:  (עזרה)
↑  Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB,  et al. (בספטמבר 2011). "Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups". Current Protocols in Bioinformatics. Chapter 6 (1): Unit 6.12.1–19. doi:10.1002/0471250953.bi0612s35. ISBN 978-0471250951. PMC 3196566. PMID 21901743. {{cite journal}}:  (עזרה)
↑  Roundup

Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (באוגוסט 2006). "Roundup: a multi-genome repository of orthologs and evolutionary distances". Bioinformatics. 22 (16): 2044–6. doi:10.1093/bioinformatics/btl286. PMID 16777906. {{cite journal}}:  (עזרה)
↑  TreeFam: Tree families database

van der Heijden RT, Snel B, van Noort V, Huynen MA (במרץ 2007). "Orthology prediction at scalable resolution by phylogenetic tree analysis". BMC Bioinformatics. 8: 83. doi:10.1186/1471-2105-8-83. PMC 1838432. PMID 17346331. {{cite journal}}:  (עזרה)
↑  TreeFam: Tree families database

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y,  et al. (בינואר 2008). "TreeFam: 2008 Update". Nucleic Acids Research. 36 (Database issue): D735-40. doi:10.1093/nar/gkm1005. PMC 2238856. PMID 18056084. {{cite journal}}:  (עזרה)
↑  Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (בינואר 2014). "TreeFam v9: a new website, more species and orthology-on-the-fly". Nucleic Acids Research. 42 (Database issue): D922-5. doi:10.1093/nar/gkt1055. PMC 3965059. PMID 24194607. {{cite journal}}:  (עזרה)
↑  OrthoFinder: Orthologs from gene trees

Emms DM, Kelly S (בנובמבר 2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology. 20 (1): 238. doi:10.1186/s13059-019-1832-y. PMC 6857279. PMID 31727128. {{cite journal}}:  (עזרה)
↑  Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (בפברואר 2009). "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates". Genome Research. 19 (2): 327–35. doi:10.1101/gr.073585.107. PMC 2652215. PMID 19029536. {{cite journal}}:  (עזרה)
↑  Thanki AS, Soranzo N, Haerty W, Davey RP (במרץ 2018). "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline". GigaScience. 7 (3): 1–10. doi:10.1093/gigascience/giy005. PMC 5863215. PMID 29425291. {{cite journal}}:  (עזרה)
↑  Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K,  et al. (בינואר 2011). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 39 (Database issue): D38-51. doi:10.1093/nar/gkq1172. PMC 3013733. PMID 21097890. {{cite journal}}:  (עזרה)
↑  Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS (במאי 2006). "Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics. 7: 270. doi:10.1186/1471-2105-7-270. PMC 1524997. PMID 16729895. {{cite journal}}:  (עזרה)
1 2  Zakany J, Duboule D (באוגוסט 2007). "The role of Hox genes during vertebrate limb development". Current Opinion in Genetics & Development. 17 (4): 359–66. doi:10.1016/j.gde.2007.05.011. PMID 17644373. {{cite journal}}:  (עזרה)
↑  Studer RA, Robinson-Rechavi M (במאי 2009). "How confident can we be that orthologs are similar, but paralogs differ?". Trends in Genetics. 25 (5): 210–6. doi:10.1016/j.tig.2009.03.004. PMID 19368988. {{cite journal}}:  (עזרה)
↑  Nehrt NL, Clark WT, Radivojac P, Hahn MW (ביוני 2011). "Testing the ortholog conjecture with comparative functional genomic data from mammals". PLOS Computational Biology. 7 (6): e1002073. Bibcode:2011PLSCB...7E2073N. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233. {{cite journal}}:  (עזרה)
↑  "Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper". 20 בספטמבר 2011. {{cite web}}:  (עזרה)
↑  Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS (ביולי 2017). "Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation". EMBO Reports. 18 (7): 1139–1149. doi:10.15252/embr.201743990. PMC 5494520. PMID 28468957. {{cite journal}}:  (עזרה)
↑  Lundin LG (באפריל 1993). "Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse". Genomics. 16 (1): 1–19. doi:10.1006/geno.1993.1133. PMID 8486346. {{cite journal}}:  (עזרה)
↑  Coulier F, Popovici C, Villet R, Birnbaum D (בדצמבר 2000). "MetaHox gene clusters". The Journal of Experimental Zoology. 288 (4): 345–51. Bibcode:2000JEZ...288..345C. doi:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y. PMID 11144283. {{cite journal}}:  (עזרה)
↑  Ruddle FH, Bentley KL, Murtha MT, Risch N (1994). "Gene loss and gain in the evolution of the vertebrates". Development. 1994: 155–61. doi:10.1242/dev.1994.Supplement.155. PMID 7579516.
↑  Pébusque MJ, Coulier F, Birnbaum D, Pontarotti P (בספטמבר 1998). "Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution". Molecular Biology and Evolution. 15 (9): 1145–59. doi:10.1093/oxfordjournals.molbev.a026022. PMID 9729879. {{cite journal}}:  (עזרה)
↑  Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (ביוני 2008). "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions". BMC Evolutionary Biology. 8 (1): 184. Bibcode:2008BMCEE...8..184L. doi:10.1186/1471-2148-8-184. PMC 2453138. PMID 18578868. {{cite journal}}:  (עזרה)
↑  Pollard SL, Holland PW (בספטמבר 2000). "Evidence for 14 homeobox gene clusters in human genome ancestry". Current Biology. 10 (17): 1059–62. Bibcode:2000CBio...10.1059P. doi:10.1016/S0960-9822(00)00676-X. PMID 10996074. {{cite journal}}:  (עזרה)
↑  Mulley JF, Chiu CH, Holland PW (ביולי 2006). "Breakup of a homeobox cluster after genome duplication in teleosts". Proceedings of the National Academy of Sciences of the United States of America. 103 (27): 10369–10372. Bibcode:2006PNAS..10310369M. doi:10.1073/pnas.0600341103. PMC 1502464. PMID 16801555. {{cite journal}}:  (עזרה)
↑  Flajnik MF, Kasahara M (בספטמבר 2001). "Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system". Immunity. 15 (3): 351–62. doi:10.1016/S1074-7613(01)00198-4. PMID 11567626. {{cite journal}}:  (עזרה)
↑  McLysaght A, Hokamp K, Wolfe KH (ביוני 2002). "Extensive genomic duplication during early chordate evolution". Nature Genetics. 31 (2): 200–4. doi:10.1038/ng884. PMID 12032567. {{cite journal}}:  (עזרה)
↑  Wolfe K (במאי 2000). "Robustness--it's not where you think it is". Nature Genetics. 25 (1): 3–4. doi:10.1038/75560. PMID 10802639. {{cite journal}}:  (עזרה)
↑  Singh PP, Affeldt S, Cascone I, Selimoglu R, Camonis J, Isambert H (בנובמבר 2012). "On the expansion of "dangerous" gene repertoires by whole-genome duplications in early vertebrates". Cell Reports. 2 (5): 1387–98. doi:10.1016/j.celrep.2012.09.034. PMID 23168259. {{cite journal}}:  (עזרה)
↑  Malaguti G, Singh PP, Isambert H (במאי 2014). "On the retention of gene duplicates prone to dominant deleterious mutations". Theoretical Population Biology. 93: 38–51. Bibcode:2014TPBio..93...38M. doi:10.1016/j.tpb.2014.01.004. PMID 24530892. {{cite journal}}:  (עזרה)
↑  Singh PP, Affeldt S, Malaguti G, Isambert H (ביולי 2014). "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLOS Computational Biology. 10 (7): e1003754. Bibcode:2014PLSCB..10E3754S. doi:10.1371/journal.pcbi.1003754. PMC 4117431. PMID 25080083. {{cite journal}}:  (עזרה)
↑  McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (בינואר 2014). "Ohnologs are overrepresented in pathogenic copy number mutations". Proceedings of the National Academy of Sciences of the United States of America. 111 (1): 361–6. Bibcode:2014PNAS..111..361M. doi:10.1073/pnas.1309324111. PMC 3890797. PMID 24368850. {{cite journal}}:  (עזרה)
↑  Makino T, McLysaght A (במאי 2010). "Ohnologs in the human genome are dosage balanced and frequently associated with disease". Proceedings of the National Academy of Sciences of the United States of America. 107 (20): 9270–4. Bibcode:2010PNAS..107.9270M. doi:10.1073/pnas.0914697107. PMC 2889102. PMID 20439718. {{cite journal}}:  (עזרה)
↑  Glover NM, Redestig H, Dessimoz C (ביולי 2016). "Homoeologs: What Are They and How Do We Infer Them?". Trends in Plant Science. Cell Press. 21 (7): 609–621. Bibcode:2016TPS....21..609G. doi:10.1016/j.tplants.2016.02.005. PMC 4920642. PMID 27021699. {{cite journal}}:  (עזרה)
1 2  García-Moreno J, Mindell DP (בדצמבר 2000). "Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD". Molecular Biology and Evolution. 17 (12): 1826–32. doi:10.1093/oxfordjournals.molbev.a026283. PMID 11110898. {{cite journal}}:  (עזרה)
עימוד רצף של חלבוני היסטון ביונקים. רצפים הם 120–180 שיירי חומצות האמינו האמצעיים של החלבונים. שאריות שנשמרו בכל הרצפים מסומנות באפור. המפתח שלמטה מציין רצף שמור (*), מוטציות שמרניות (:), מוטציות שמרניות למחצה (.) ומוטציות לא שמרניות ( ).
למעלה: גן קדמון משתכפל כדי לייצר שני פאראלוגים (גנים A ו-B). אירוע ספציאציה מייצר אורתולוגים בשני מיני הבת. למטה: במין נפרד, לגן לא קשור יש תפקיד דומה (גן C) אבל יש לו מקור אבולוציוני נפרד וכך הוא אנלוגי.
גני HOX של בעלי חוליות מאורגנים בקבוצות של פאראלוגים. כל צביר הוקס (HoxA, HoxB וכו') נמצא על כרומוזום אחר. לדוגמה, צביר HoxA האנושי נמצא על כרומוזום 7. לצביר HoxA של העכבר המוצג כאן יש 11 גנים פאראלוגיים (2 חסרים).