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<!DOCTYPE html> <html lang="en-gb"> <head> <title>Whole genome alignment</title> <link rel="stylesheet" type="text/css" media="all" href="/minified/1627d0642fc0489f4d5171e89c120c90.css"/><link rel="stylesheet" type="text/css" media="all" href="/minified/1e7dbc57580167c82fbefd42000cbfd3.image.css"/> <link rel="icon" type="image/png" href="/i/ensembl-favicon.png" /> <link rel="apple-touch-icon" href="/apple-touch-icon.png" type="image/png" /> <link href="//metazoa.ensembl.org/opensearch/all.xml" type="application/opensearchdescription+xml" rel="search" title="Ensembl (All)" /> <meta name="description" content="Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest" /> <meta name="viewport" content="target-densitydpi=device-dpi, width=device-width, initial-scale=1.0, maximum-scale=2.0, user-scalable=yes" /> <script>var prefetch = [];</script> </head> <body class="ie ie7 ie67 static" data-pace="2" id="ensembl-webpage"> <div id="min_width_container"> <div id="min_width_holder">   <div id="masthead" class="js_panel"> <input type="hidden" class="panel_type" value="Masthead" /> <div class="logo_holder"><a href="/"><img src="/i/e.png" alt="Ensembl Genomes Home" title="Ensembl Genomes Home" class="print_hide" style="width:43px;height:40px" /></a><a href="/"><img src="/i/ensemblMetazoa.png" alt="Ensembl Metazoa Home" title="Ensembl Metazoa Home" class="print_hide" style="width:195px;height:40px" /></a><img src="/i/e-ensembl_print.gif" alt="Ensembl Metazoa Home" title="Ensembl Metazoa Home" class="screen_hide_inline" style="width:195px;height:40px" /> <span class="print_hide"> <span id="site_menu_button">▼</span> <ul id="site_menu" style="display:none"> <li><a href="http://www.ensemblgenomes.org">Ensembl Genomes</a></li> <li><a href="http://bacteria.ensembl.org">Ensembl Bacteria</a></li> <li><a href="http://protists.ensembl.org">Ensembl Protists</a></li> <li><a href="http://fungi.ensembl.org">Ensembl Fungi</a></li> <li><a href="http://plants.ensembl.org">Ensembl Plants</a></li> <li><a href="http://metazoa.ensembl.org">Ensembl Metazoa</a></li> <li><a href="http://www.ensembl.org">Ensembl (vertebrates)</a></li> </ul> </span> </div> <div class="mh print_hide"> <div class="account_holder"><div class="_account_holder"><div class="account-loading">Loading…</div><form action="/Ajax/accounts_dropdown"></form></div></div> <div class="tools_holder"><ul class="tools"><li><a class="constant" href="/hmmer">HMMER</a></li><li><a class="constant" href="/Multi/Tools/Blast">BLAST</a></li><li><a class="constant" href="/biomart/martview">BioMart</a></li><li><a class="constant" href="/tools.html">Tools</a></li><li><a class="constant" href="/info/data/ftp/index.html">Downloads</a></li><li><a class="constant" href="/info/">Help & Docs</a></li><li class="last"><a class="constant" target="_blank" href="http://www.ensembl.info">Blog</a></li></ul><div class="more"><a href="#">More <span class="arrow">▼</span></a></div></div> <div class="search_holder print_hide"> <div id="searchPanel" class="js_panel"> <input type="hidden" class="panel_type" value="SearchBox" /> <form action="/Multi/Psychic"> <div class="search print_hide"> <div class="sites button"> <img class="search_image no-sprite badge-16" src="/i/search/ensemblunit.gif" alt="" /> <img src="/i/search/down.gif" style="width:7px" alt="" /> <input type="hidden" name="site" value="ensemblunit" /> </div> <div> <label class="hidden" for="se_q">Search terms</label> <input class="query inactive" id="se_q" type="text" name="q" value="Search Ensembl Metazoa…" data-role="none" onkeydown="if (event.keyCode == 13) { $(this).closest('form').submit(); 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LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions.</p> <p>The raw results from LastZ or tBLAT are alignment blocks, which are 'chained' according to their location in both genomes, then 'netted' to choose the best sub-chain in each region for the reference species [4]. The resultant <b>LastZ-net</b> and <b>tBLAT-net</b> alignments are displayed in Ensembl Genomes for selected <a href="http://fungi.ensembl.org/info/genome/compara/compara_analyses.html">fungal</a>, <a href="http://metazoa.ensembl.org/info/genome/compara/compara_analyses.html">metazoan</a>, <a href="http://protists.ensembl.org/info/genome/compara/compara_analyses.html">protist</a> and <a href="http://plants.ensembl.org/info/genome/compara/compara_analyses.html">plant</a> species.</p> <h2>References</h2> <ol> <li><a href="http://www.bx.psu.edu/~rsharris/lastz">Improved pairwise alignment of genomic DNA</a>. Harris RS. 2007. Ph.D. Thesis, The Pennsylvania State University.</li> <li><a href="http://europepmc.org/abstract/MED/12529312">Human-mouse alignments with BLASTZ</a>. Schwartz S <em>et al</em>. 2003. Genome Research. 13(1):103-7.</li> <li><a href="http://europepmc.org/abstract/MED/11932250">BLAT--the BLAST-like alignment tool</a>. Kent WJ. 2002. Genome Research. 12(4):656-64.</li> <li><a href="http://europepmc.org/abstract/MED/14500911">Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</a>. Kent WJ <em>et al</em>. 2003. PNAS. 100(20):11484-9.</li> </ol> </div></div> </div> <div id="footer"> <div class="column-wrapper"> <div class="column-two left"> <p> Ensembl Metazoa release 60 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" style="white-space:nowrap">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI</span> </p> </div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div id="fat-footer"> <div class="column-four left"> <h3>About Us</h3> <p><a href="/info/about/">About us</a></p> <p><a href="/info/about/contact/">Contact us</a></p> <p><a href="/info/about/publications.html">Citing Ensembl Genomes</a></p> <p><a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice">Privacy policy</a></p> <p><a href="/info/about/legal/">Disclaimer</a></p> </div> <div class="column-four left"> <h3>Get help</h3> <p><a href="/info/website/">Using this website</a></p> <p><a href="/info/">Documentation</a></p> <p><a href="/info/website/upload/">Adding 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id="hidden_species_list" name="hidden_species_list" value=Glossina_morsitans|Megaselia_scalaris|Pomacea_canaliculata_gca003073045v1|Ascaris_suum_prjna62057|Tetranychus_urticae|Bombus_impatiens_gca000188095v4|Drosophila_innubila_gca004354385v1rs|Echinococcus_granulosus_gca000524195v1rs|Mytilus_californianus_gca021869535v1rs|Homarus_gammarus_gca958450375v1|Amyelois_transitella_gca001186105v1rs|Apis_dorsata_gca000469605v1rs|Neodiprion_lecontei_gca021901455v1rs|Drosophila_guanche_gca900245975v1rs|Bemisia_tabaci_uganda1|Adineta_vaga|Hyalomma_asiaticum_gca013339685v1|Cherax_quadricarinatus_gca026875155v2rs|Galendromus_occidentalis_gca000255335v2rs|Anthonomus_grandis_gca022605725v3rs|Drosophila_virilis|Amblyteles_armatorius_gca933228735v1|Orussus_abietinus_gca000612105v2|Lottia_gigantea|Dreissena_polymorpha_gca020536995v1rs|Amphibalanus_amphitrite_gca019059575v1|Limnoperna_fortunei_gca944474755v1|Drosophila_pseudoobscura_gca009870125v2rs|Eriocheir_sinensis_gca024679095v1rs|Schistocerca_piceifrons_gca021461385v2rs|Bemisia_tabaci_ssa2nig|Thelohanellus_kitauei|Harpegnathos_saltator_gca003227715v2rs|Camponotus_floridanus_gca003227725v1rs|Drosophila_persimilis_gca003286085v2rs|Clytia_hemisphaerica_gca902728285|Pomphorhynchus_laevis_gca012934845v2gb|Ixodes_scapularis_ise6|Hydra_vulgaris_gca022113875v1rs|Actinia_tenebrosa_gca009602425v1|Ooceraea_biroi_gca003672135v1|Schistosoma_haematobium_gca000699445v2rs|Oppia_nitens_gca028296485v1rs|Polistes_fuscatus_gca010416935v1rs|Topomyia_yanbarensis_gca030247195v1rs|Ctenocephalides_felis_gca003426905v1rs|Varroa_jacobsoni_gca002532875v1rs|Anastrepha_ludens_gca028408465v1rs|Lucilia_cuprina|Diaphorina_citri_gca000475195v1rs|Drosophila_suzukii_gca013340165v1rs|Melanaphis_sacchari_gca002803265v2rs|Rhopalosiphum_maidis_gca003676215v3|Copidosoma_floridanum_gca000648655v2|Phlebotomus_papatasi_gca024763615v2rs|Aedes_albopictus|Patella_vulgata_gca932274485v1|Microctonus_aethiopoides_gca030347275v1cm|Daphnia_magna_gca020631705v2|Stegodyphus_mimosarum|Orbicella_faveolata_gca002042975v1|Coremacera_marginata_gca914767935v1|Drosophila_rhopaloa_gca018152115v1rs|Homarus_americanus_gca018991925v1|Nasonia_vitripennis|Hymenolepis_microstoma_prjeb124|Ixodes_scapularis_gca016920785v2|Anopheles_quadriannulatus|Eurytemora_affinis_gca000591075v2|Drosophila_takahashii_gca018152695v1rs|Drosophila_obscura_gca018151105v1rs|Diabrotica_virgifera_gca917563875v2rs|Limnephilus_rhombicus_gca929108145v2|Bombus_terrestris|Pocillopora_damicornis_gca003704095v1|Sarcoptes_scabiei_gca014595675v1|Helicoverpa_zea_gca022581195v1rs|Lutzomyia_longipalpis_gca024334085v1rs|Caenorhabditis_japonica_prjna12591|Diuraphis_noxia_gca001186385v1|Strongyloides_ratti_prjeb125|Glossina_palpalis|Drosophila_melanogaster|Drosophila_ananassae|Drosophila_eugracilis_gca018153835v1rs|Brugia_malayi_prjna10729|Leptotrombidium_deliense|Drosophila_yakuba_gca016746365v2rs|Daphnia_pulex_gca021134715v1rs|Teleopsis_dalmanni_gca002237135v2|Acromyrmex_echinatior_gca000204515v1rs|Bactrocera_tryoni_gca016617805v2|Drosophila_biarmipes_gca025231255v1rs|Daktulosphaira_vitifoliae_gca025091365v1rs|Anopheles_merus|Rhipicephalus_sanguineus_gca013339695v2rs|Dermatophagoides_pteronyssinus_gca001901225v2|Dermacentor_andersoni_gca023375885v2rs|Glossina_austeni|Drosophila_virilis_gca003285735v2rs|Anopheles_sinensis|Drosophila_pseudoobscura|Phlebotomus_perniciosus_GCA_918844115.2|Malaya_genurostris_gca030247185v2rs|Dendronephthya_gigantea_gca004324835v1|Lucilia_cuprina_gca022045245v1rs|Dufourea_novaeangliae_gca001272555v1rs|Haliotis_rubra_gca003918875v1rs|Drosophila_grimshawi_gca018153295v1rs|Machimus_atricapillus_gca933228815v1|Octopus_bimaculoides_gca001194135v2rs|Drosophila_mojavensis|Anopheles_albimanus|Helobdella_robusta|Trichuris_muris_prjeb126|Asterias_rubens_GCA_902459465.3|Lineus_longissimus_gca910592395v2|Anopheles_melas|Habropoda_laboriosa_gca001263275v1rs|Crassostrea_gigas|Nilaparvata_lugens_gca014356525v1rs|Limulus_polyphemus_gca000517525v1|Drosophila_kikkawai_gca018152535v1rs|Agrilus_planipennis_gca000699045v2|Microplitis_demolitor_gca026212275v2rs|Macrosteles_quadrilineatus_gca028750875v1rs|Rhagoletis_pomonella_gca013731165v1|Orchesella_cincta|Anopheles_stephensi|Culex_quinquefasciatus|Neodiprion_pinetum_gca021155775v1rs|Mayetiola_destructor|Pediculus_humanus|Onthophagus_taurus_gca000648695v2|Patella_pellucida_gca917208275v1|Culex_quinquefasciatus_gca015732765v1vb|Drosophila_miranda_gca003369915v2rs|Drosophila_mojavensis_gca018153725v1rs|Cotesia_glomerata_gca020080835v1|Branchiostoma_lanceolatum|Drosophila_subpulchrella_gca014743375v2rs|Caenorhabditis_elegans|Bemisia_tabaci_ssa3nig|Drosophila_teissieri_gca016746235v2rs|Dimorphilus_gyrociliatus_gca904063045v1|Anopheles_dirus|Anopheles_coluzzii_ngousso|Diorhabda_carinulata_gca026250575v1rs|Manduca_sexta_gca014839805v1rs|Drosophila_persimilis|Heliconius_melpomene|Anopheles_stephensi_indian|Galleria_mellonella_gca003640425v2rs|Myopa_tessellatipennis_gca943737955v1|Penaeus_chinensis_gca019202785v2rs|Phlebotomus_papatasi|Lingula_anatina_gca001039355v2|Mya_arenaria_gca026914265v1rs|Stylophora_pistillata_gca002571385v1|Nematostella_vectensis|Acyrthosiphon_pisum_gca005508785v2rs|Drosophila_sechellia_gca004382195v2rs|Bemisia_tabaci_ssa1nig|Anneissia_japonica_gca011630105v1|Plodia_interpunctella_gca027563975v1rs|Drosophila_hydei_gca003285905v2rs|Daphnia_carinata_gca022539665v3rs|Limnephilus_marmoratus_gca917880885v1|Megachile_rotundata_gca000220905v1rs|Pecten_maximus_gca902652985v1rs|Bicyclus_anynana_gca900239965v1rs|Homalodisca_vitripennis_gca021130785v2rs|Acanthaster_planci_gca001949145v1|Dendroctonus_ponderosae_gca000355655v1|Microctonus_aethiopoides_gca030272935v1cm|Sitophilus_oryzae_gca002938485v2rs|Trichogramma_pretiosum_gca000599845v3|Anopheles_epiroticus|Ceratitis_capitata_gca000347755v4|Loa_loa|Bombus_affinis_gca024516045v2rs|Belgica_antarctica|Ancistrocerus_nigricornis_gca916049575v1|Drosophila_busckii_gca011750605v1rs|Stegodyphus_dumicola_gca010614865v2rs|Anoplophora_glabripennis_gca000390285v2|Octopus_sinensis_gca006345805v1|Penaeus_monodon_gca015228065v1|Musca_domestica|Bemisia_tabaci_asiaii5|Amphimedon_queenslandica_gca000090795v2rs|Drosophila_ficusphila_gca018152265v1rs|Sipha_flava_gca003268045v1|Daphnia_pulicaria_gca021234035v2rs|Schistocerca_gregaria_gca023897955v2rs|Limnephilus_lunatus_gca917563855v2|Melitaea_cinxia_gca905220565v1|Caenorhabditis_brenneri_prjna20035|Drosophila_willistoni_gca018902025v2rs|Aphidius_gifuensis_gca014905175v1|Culex_pipiens_gca016801865v2rs|Drosophila_elegans_gca000224195v2rs|Hypsibius_exemplaris_gca002082055v1|Drosophila_ananassae_gca017639315v2rs|Danaus_plexippus_gca009731565v1|Crassostrea_angulata_gca025612915v2rs|Anopheles_coluzzii|Drosophila_subobscura_gca008121235v1rs|Lytechinus_variegatus_gca018143015v1|Toxorhynchites_rutilus_gca029784135v1rs|Drosophila_willistoni|Drosophila_erecta_gca003286155v2rs|Apis_florea_gca000184785v2rs|Hylaeus_volcanicus_gca026283585v1rs|Panonychus_citri_gca014898815v1rs|Anopheles_funestus_gca943734845v1rs|Venturia_canescens_gca019457755v1rs|Ichneumon_xanthorius_gca917499995v1|Pristionchus_pacificus_prjna12644|Solenopsis_invicta_gca016802725v1|Trichinella_spiralis|Lutzomyia_longipalpis|Drosophila_simulans|Athalia_rosae_gca917208135v1|Actinia_equina_GCA_011057435.1|Drosophila_navojoa_gca001654015v2rs|Caenorhabditis_briggsae_prjna10731|Schistocerca_cancellata_gca023864275v2rs|Polistes_dominula_gca001465965v1rs|Drosophila_bipectinata_gca000236285v2rs|Pectinophora_gossypiella_gca024362695v1rs|Patiria_miniata_gca015706575v1|Polistes_canadensis_gca001313835v1rs|Necator_americanus_prjna72135|Anopheles_gambiae|Drosophila_erecta|Hermetia_illucens_gca905115235v1|Adelges_cooleyi_gca023614345v1rs|Hyalella_azteca_gca000764305v2|Strigamia_maritima|Haliotis_rufescens_gca023055435v1rs|Anopheles_christyi|Spodoptera_frugiperda_gca023101765v3rs|Monomorium_pharaonis_gca013373865v2|Bombus_terrestris_gca910591885v2|Anopheles_arabiensis|Priapulus_caudatus_gca000485595v2|Culicoides_sonorensis|Glossina_pallidipes|Microctonus_hyperodae_gca030347285v1cm|Atta_cephalotes|Cryptotermes_secundus_gca002891405v2rs|Glyphotaelius_pellucidus_gca936435175v1|Bactrocera_latifrons_gca001853355v1|Thrips_palmi_gca012932325v1rs|Zerene_cesonia_gca012273895v2rs|Chelonus_insularis_gca013357705v1rs|Cataglyphis_hispanica_gca021464435v1rs|Ixodes_persulcatus_gca013358835v1|Mercenaria_mercenaria_gca014805675v2|Varroa_destructor_gca002443255|Schistocerca_americana_gca021461395v2rs|Drosophila_sechellia|Drosophila_arizonae_gca001654025v1rs|Rhodnius_prolixus|Anopheles_funestus|Uloborus_diversus_gca026930045v1rs|Leguminivora_glycinivorella_gca023078275v1rs|Biomphalaria_glabrata|Cimex_lectularius|Wyeomyia_smithii_gca029784165v1rs|Rhipicephalus_microplus_gca013339725v1|Apis_mellifera|Dermacentor_silvarum_gca013339745v2rs|Ostrea_edulis_gca023158985v1rs|Bombyx_mandarina_gca003987935v1rs|Glossina_fuscipes_gca014805625v1|Anopheles_minimus|Folsomia_candida|Penaeus_vannamei_gca003789085v1|Ixodes_scapularis|Parasteatoda_tepidariorum_gca000365465v3|Aplysia_californica_gca000002075v2|Drosophila_grimshawi|Zootermopsis_nevadensis|Tribolium_castaneum|Trichoplax_adhaerens|Linepithema_humile_gca000217595v1rs|Portunus_trituberculatus_gca017591435v1|Bombyx_mori_gca014905235v2|Hylaeus_anthracinus_gca026225885v1rs|Paramacrobiotus_metropolitanus_gca019649055v1rs|Dinothrombium_tinctorium|Hofstenia_miamia|Bactrocera_neohumeralis_gca024586455v2rs|Lepeophtheirus_salmonis_gca016086655v3rs|Anopheles_culicifacies|Acropora_millepora_gca013753865v1|Schistocerca_nitens_gca023898315v2rs|Diorhabda_sublineata_gca026230105v1rs|Bombus_vancouverensis_gca011952275v1rs|Anopheles_maculatus|Zeugodacus_cucurbitae_gca028554725v2rs|Hydractinia_symbiolongicarpus_gca029227915v2rs|Helicoverpa_armigera_gca023701775v1rs|Schistosoma_mansoni_prjea36577|Gigantopelta_aegis_gca016097555v1|Microplitis_mediator_gca029852145v1rs|Tribolium_madens_gca015345945v1rs|Anopheles_darlingi|Uranotaenia_lowii_gca029784155v1rs|Anastrepha_obliqua_gca027943255v1rs|Penaeus_japonicus_gca017312705v1|Onchocerca_volvulus_prjeb513|Drosophila_santomea_gca016746245v2rs|Haemaphysalis_longicornis_gca013339765v1|Crassostrea_virginica_gca002022765v4|Phlebotomus_argentipes_gca947086385v1rs|Aethina_tumida_gca024364675v1rs|Eufriesea_mexicana_gca001483705v1rs|Bemisia_tabaci_ssa1ug|Drosophila_mauritiana_gca004382145v1rs|Bactrocera_dorsalis_gca000789215v2|Caenorhabditis_remanei_prjna53967|Schistocerca_serialis_gca023864345v3rs|Pogonomyrmex_barbatus_gca000187915v1rs|Drosophila_gunungcola_gca025200985v1rs|Tigriopus_californicus_gca007210705|Microctonus_aethiopoides_gca030272655v1cm|Saccoglossus_kowalevskii_gca000003605v1|Anopheles_atroparvus_GCA_914969975.1|Aedes_aegypti_lvpagwg|Glossina_brevipalpis|Leptinotarsa_decemlineata_gca000500325v2|Mizuhopecten_yessoensis_gca002113885v2|Pollicipes_pollicipes_gca011947565v2|Anopheles_farauti|Strongylocentrotus_purpuratus|Mnemiopsis_leidyi|Stomoxys_calcitrans|Anopheles_sinensis_china|Cylas_formicarius_gca029955315v1rs|Lytechinus_pictus_gca015342785v2rs|Owenia_fusiformis_gca903813345v1|Capitella_teleta|Centruroides_sculpturatus_gca000671375v2|Diabrotica_virgifera_gca003013835v2|Drosophila_albomicans_gca009650485v2rs|Procambarus_clarkii_gca020424385v2|Anopheles_coluzzii_gca943734685v1rs|Halyomorpha_halys_gca000696795v2rs|Exaiptasia_diaphana_gca001417965v1|Bombus_huntii_gca024542735v1rs|Trialeurodes_vaporariorum_gca011764245|Drosophila_simulans_gca016746395v2rs> 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