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added primerschemes designed with varVAMP (#43)
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| # varvamp-hav 1000bp v1.0.0 | ||
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| [primalscheme labs](https://labs.primalscheme.com/detail/varvamp-hav/1000/v1.0.0) | ||
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| ## Description | ||
|
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||
| Pan-specfic primer scheme for HAV designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates. | ||
|
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| ## Overviews | ||
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|  | ||
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| ## Details | ||
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| ```json | ||
| { | ||
| "ampliconsize": 1000, | ||
| "schemeversion": "v1.0.0", | ||
| "schemename": "varvamp-hav", | ||
| "primer_bed_md5": "06852b6301eb63495d9c2625b0e7f40c", | ||
| "reference_fasta_md5": "d65a09200bbec78ffa410740ba3143ff", | ||
| "status": "validated", | ||
| "citations": [], | ||
| "authors": [ | ||
| "Jonas Fuchs" | ||
| ], | ||
| "algorithmversion": "varVAMP:0.8.3", | ||
| "species": [ | ||
| 470424 | ||
| ], | ||
| "license": "CC BY-SA 4.0", | ||
| "primerclass": "primerschemes", | ||
| "infoschema": "v2.0.0", | ||
| "articbedversion": "v2.0", | ||
| "collections": [ | ||
| "WHOLE-GENOME", | ||
| "CLINICAL-ISOLATES", | ||
| "COMMUNITY" | ||
| ], | ||
| "links": { | ||
| "protocols": [], | ||
| "validation": [ | ||
| "https://www.biorxiv.org/content/10.1101/2024.05.08.593102v1.full" | ||
| ], | ||
| "homepage": [ | ||
| "https://github.com/jonas-fuchs/ViralPrimerSchemes/tree/main/varvamp_tiled/HAV" | ||
| ], | ||
| "vendors": [], | ||
| "misc": [] | ||
| }, | ||
| "description": "Pan-specfic primer scheme for HAV designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates.", | ||
| "derivedfrom": null, | ||
| "contactinfo": "[email protected]" | ||
| } | ||
| ``` | ||
|
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||
|
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||
|
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| ------------------------------------------------------------------------ | ||
|
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| This work is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/) | ||
|
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|  |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| { | ||
| "ampliconsize": 1000, | ||
| "schemeversion": "v1.0.0", | ||
| "schemename": "varvamp-hav", | ||
| "primer_bed_md5": "06852b6301eb63495d9c2625b0e7f40c", | ||
| "reference_fasta_md5": "d65a09200bbec78ffa410740ba3143ff", | ||
| "status": "validated", | ||
| "citations": [], | ||
| "authors": [ | ||
| "Jonas Fuchs" | ||
| ], | ||
| "algorithmversion": "varVAMP:0.8.3", | ||
| "species": [ | ||
| 470424 | ||
| ], | ||
| "license": "CC BY-SA 4.0", | ||
| "primerclass": "primerschemes", | ||
| "infoschema": "v2.0.0", | ||
| "articbedversion": "v2.0", | ||
| "collections": [ | ||
| "WHOLE-GENOME", | ||
| "CLINICAL-ISOLATES", | ||
| "COMMUNITY" | ||
| ], | ||
| "links": { | ||
| "protocols": [], | ||
| "validation": [ | ||
| "https://www.biorxiv.org/content/10.1101/2024.05.08.593102v1.full" | ||
| ], | ||
| "homepage": [ | ||
| "https://github.com/jonas-fuchs/ViralPrimerSchemes/tree/main/varvamp_tiled/HAV" | ||
| ], | ||
| "vendors": [], | ||
| "misc": [] | ||
| }, | ||
| "description": "Pan-specfic primer scheme for HAV designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates.", | ||
| "derivedfrom": null, | ||
| "contactinfo": "[email protected]" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,14 @@ | ||
| ambiguous_consensus 164 186 HAV_0_LEFT_1 0 + GGCGGGGTCAACTCCATGATTA | ||
| ambiguous_consensus 1567 1590 HAV_0_RIGHT_1 0 - TGNCCAACYGARTCHGAAGCATT | ||
| ambiguous_consensus 2225 2247 HAV_1_LEFT_1 0 + TGGATRTTTCAGGWGTVCAAGC | ||
| ambiguous_consensus 3394 3417 HAV_1_RIGHT_1 0 - TGWGGRAAATTMACTTTRGACCA | ||
| ambiguous_consensus 4170 4194 HAV_2_LEFT_1 0 + TGTYCAYTCAATGGCWCARGTTGA | ||
| ambiguous_consensus 5271 5295 HAV_2_RIGHT_1 0 - RGCATTCATRACCCATCTMACACA | ||
| ambiguous_consensus 5700 5722 HAV_3_LEFT_1 0 + GGTCTYCCWGGRATGTGYGGTG | ||
| ambiguous_consensus 7130 7152 HAV_3_RIGHT_1 0 - AYTCAGCRTTRCTTCTYTGCCA | ||
| ambiguous_consensus 1435 1459 HAV_4_LEFT_1 1 + GCWAGRGCAAARATGTCTTTTGCT | ||
| ambiguous_consensus 2560 2580 HAV_4_RIGHT_1 1 - GCCATDCCATCHACATCAGT | ||
| ambiguous_consensus 3281 3303 HAV_5_LEFT_1 1 + TGGATGCTGGRGTTCTKACTGG | ||
| ambiguous_consensus 4430 4453 HAV_5_RIGHT_1 1 - CATCCCARTAATCWGARGCMACA | ||
| ambiguous_consensus 4954 4978 HAV_6_LEFT_1 1 + CARTCTTTTCCMTCTGGTGARCCA | ||
| ambiguous_consensus 6134 6156 HAV_6_RIGHT_1 1 - GCCCCWGTWATRGCCATWTCAA |
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| >ambiguous_consensus | ||
| NNNNGGCTWHDYBYNNYCCYTNTYYNNBYDTYNNGTAAATATWRATTCCTGCAGGTTCAG | ||
| GKYTCNTYDRATYNTGTTYCWCTWTAWGNRACACTCNTTTCACGCTTTCTGTCTBCNTTT | ||
| CTTCCAGGGCTCTCCCCTTGCCCTAGGCTCTGGCCGTTGCGCCCGGCGGGGTCAACTCCA | ||
| TGATTAGCATGGAGCTGTAGGAGTCTAAATTGGGGACRCAGATGTTKGGRACGTCRCCTT | ||
| GCAGTGTTAACTTGGCTYNTCATGAABCTYTTTGATCTTCCACAAGRGGTAGGCTACGGG | ||
| TGAAACCTCTTARGCTAATACTTCTATGAAGAGATGCYTTGGATAGGGTAACAGCGGCGG | ||
| AYATTGGTGAGTTGTTNWGACAAAAACCATTCAACGCCGGAGGACTGRCTCTCATCCAGT | ||
| GGATGCATTRAGTGRATTGWYTGTYAGGGCTGTCTYTAGGYTTAATYYCNWGACCTCTCT | ||
| GTGCTTRGGGCAAACAHHNAYTTGGCCTTAAATGRGRTYCTGTGAGAGGGGRYNCYCKCC | ||
| ATTGAMWGCTGGACWKTTCTTTGGGGCCTTNTGTDKTNGTTTGCCKCTGAGGTACTCAGG | ||
| GGCATTTAGGTTTTTCCTCATYHWYANAAYAATWATGAAYATGTCYARACARGGWATTTT | ||
| YCAGACTGTTGGGAGTGGYCTTGACCACATCCTGTCTYTGGCAGAYRTKGAGGARGARCA | ||
| AATGATYCARTCHGTKGATMGKACYGCAGTKACTGGDGCTTCWTAYTTYACKTCTGTKGA | ||
| YCAATCTTCWGTTCAYACWGCTGARGTTGGHTCACAYCARVYTGAACCTYTGARAACYTC | ||
| WGTTGAYAAACCHGGYTCHAARARRACHCARGGRGARAARTTTTTCYTKATTCATTCTGC | ||
| WGATTGGYTBACBACACATGCTYTBTTYCATGAAGTTGCAAAATTGGATGTGGTVARRYT | ||
| RYTRTAYAATGARCARTTTGCYGTYCARGGBYTGTTGAGRTAYCAYACWTATGCAAGATT | ||
| TGGMATTGARATWCAAGTTCAGATMAAYCCYACWCCHTTYCARCARGGDGGDYTRATHTG | ||
| TGCYATGGTKCCWGGWGAYCARAGYTATGGWTCDATAGCWTCHYTGACWGTTTATCCYCA | ||
| TGGYYTGTTRAATTGYAAYATYAAYAATGTRGTYAGAATWAAGGTTCCWTTYATTTAYAC | ||
| WAGRGGWGCTTAYCAYTTYAARGAYCCWCARTAYCCWGTYTGGGARTTRACWATYAGAGT | ||
| YTGGTCWGARYTRAAYATTGGRACWGGWACYTCHGCTTAYACWTCACTBAATGTBTTRGC | ||
| TAGRTTYACWGATTTGGARYTVCATGGRTTRACWCCTCTKTCYACACARATGATGAGRAA | ||
| TGAATTTAGRGTYAGTACHACWGARAATGTKGTDAATYTGTCMAATTATGAAGATGCWAG | ||
| RGCAAARATGTCTTTTGCTYTDGAYCARGAAGAYTGGAARTCTGATSCBTCYCARGGBGG | ||
| WGGRATYAAAATYACWCATTTTACWACYTGGACATCHATTCCMACYTTRGCTGCYCAGTT | ||
| TCCATTYAATGCTTCDGAYTCRGTTGGNCARCARATYAARGTTATWCCAGTKGAYCCATA | ||
| YTTYTTYCARATGACWAAYACWAAYCCTGAYCARAAATGTATAACTGCHYTGGCYTCHAT | ||
| HTGTCARATGTTTTGYTTYTGGAGRGGAGAYCTKGTYTTTGAYTTYCARGTTTTTCCHAC | ||
| MAAATATCATTCAGGHAGRYTRYTRTTTTGYTTTGTTCCTGGNAATGARYTRATWGATGT | ||
| YWCYSRMATHACAYTRAARCARGCMACYACTGCBCCYTGTGCWGTRATGGAYATWACWGG | ||
| AGTRCARTCAACYTTGAGATTTCGTGTTCCYTGGATTTCWGAYACWCCYTAYMGRGTDAA | ||
| YAGRTAYACVAARTCRKCACATCARAARGGHGARTAYACTGCYATWGGRAAGYTKATTGT | ||
| KTAYTGYTAYAAYAGAYTGACYTCTCCYTCYAAYGTKGCTTCYCATGTYAGRGTDAATGT | ||
| TTAYCTYTCAGCWATTAAYTTGGARTGYTTTGCTCCWCTYTAYCATGCHATGGATGTYAC | ||
| HACWCARGTTGGAGATGATTCWGGRGGYTTYTCWACVACWGTYTCWACARARCAGAATGT | ||
| TCCWGAYCCHCAAGTYGGYATWACAACHRTGARRGAYYTDAAAGGDARAGCHAAYMRRGG | ||
| RAARATGGATRTTTCAGGWGTVCAAGCWCCTNGTGGGAGCWATYANCWACMATTGARNGA | ||
| TCCAGTTTTRGCAAAGAAAGTRCCTGARACWTTYCCWGAATTGAARCCTGGAGARTCHAG | ||
| RCAYACWTCWGATCAYATGTCYATYTAYAARTTYATGGGVAGRTCTCAYTTYYTRTGYAC | ||
| WTTYACHTTYAATTCWAAYAAYAARGAGTACACWTTTCCWATWACYYTGTCWTCRACYTC | ||
| HAATCCTCCWCATGGWTTRCCWTCHACWYTRAGRTGGTTYTTYAAYYTKTTYCARYTKTA | ||
| TAGRGGDCCWTTRGAYYTRACAATWATWATHACWGGRGCHACTGATGTDGATGGHATGGC | ||
| YTGGTTYACWCCWGTDGGBYTKGCHGTHGAYACNCCYTGGGTDGARAAGGARTCWGCYYT | ||
| DTCYATTGAYTAYAARACWGCYCTTGGWGCTGTYAGRTTYAAYACMAGRAGAACAGGRAA | ||
| YATTCAGATYAGRYTRCCDTGGTAYTCYTATYTDTATGCYGTKTCWGGRGCAYTGGATGG | ||
| BYTKGGAGAYAARACRGATTCHACWTTTGGAYTKGTYTCYATTCARATTGCAAATTAYAA | ||
| TCAYTCWGAYGAATAYTTGTCYTTTAGTTGYTAYTTRTCTGTBACWGARCARTCWGAGTT | ||
| YTATTTTCCYAGAGCWCCWTTRAAYWCMAATGCYATGWTRTCMWCTGARWCMATGATGRR | ||
| YAGAATTGCWSYTGGWGAYYTKGARTCMTCRGTKGATGATCCYMGATCWGARGARGAYMR | ||
| WARATTTGARAGTCAYATWGAAWRBAGRAARCCWTAYAAAGARYTRAGAYTRGARGTTGG | ||
| NAARCAAAGACTHAARTATGCTCAGGAAGARTTRTCAAATGAAGTRYTKCCWCCYCCTMG | ||
| KAAAATKAARGGDBTRTTTTCACAAGCHAARATYTCWYTKTTTTAYACWGARGAKCATGA | ||
| AATWATGAARTTYTCYTGGARAGGWRTDACTGCTGAYACTAGRGCTYTRAGRAGRTTTGG | ||
| MTTYTCWHTRGCYGCWGGBAGRAGTGTGTGGACWCTKGARATGGATGCTGGRGTTCTKAC | ||
| TGGVAGRYTGRTBAGRBTSAATGATGARAAATGGACRGAAATGAARGATGAYAARATHGT | ||
| YTCWTTRRTBGARAARTTYACWAGYAAYAARYAYTGGTCYAAAGTKAATTTYCCWCATGG | ||
| VATGYTRGATYTKGAAGARATTGCTGCHAAYTCHAARGAHTTTCCWAAYATGTCWGARAC | ||
| DGAYTTGTGTTTCYTRYTSCATTGGYTRAATCCMAAGAARATHAAYTTRGCAGAYAGAAT | ||
| GYTKGGWYTRTCWGGRRTDCARGAAATWAAAGAAMARGGWGTKGGAYTRATWGSWGAGTG | ||
| YMGARCTTTYYTRGATTCWATWRCTRGDACTYTRAARTCHATGATGTTTGGDTTTCATCA | ||
| YTCTGTVACWGTTGAAATYATWAAYACTGTDYTBTGYTTTGTYAARAGTGGMATYYTRCT | ||
| DTATGTHATWCAACAATTRAAYCARGAKGARCAYTCYCAYATAATTGGYYTGTTGAGAGT | ||
| BATGAATTATGYWGAYATTGGBTGYTCWGTYATYTCATGTGGYAAAGTKTTYTCHAAAAT | ||
| GYTRGAAACWGTBTTTAATTGGCARATGGAYTCBAGAATGATGGAGYTVAGRACWCAGAG | ||
| YWTYTCHAAYTGGYTWAGRGAYATYTGTTCWGGDATHACHATTTTTAARARYTTYAARGA | ||
| TGCMATWTATTGGYTWTAYACAAAAWTVARRGAHTWTTATGAHSTRAATTATGGYAADAA | ||
| RAAGGAYRTTYTWAAYATTCTBAARGAYMAYCARCARAAAATWGARARAGCYATTGARGA | ||
| RGCHGAYAAWTTYTGYRTTYTKCARATYCARGATGTDGARAARTYTGAWCAGTAYCARAA | ||
| AGGRGTWGAYTTRATWCAAAARYTGAGRACTGTYCAYTCAATGGCWCARGTTGAYCCHRR | ||
| YYTDRBKGTYCATTTRKCMCCTYTBAGAGAYTGYATWGCHAGAGTYCAYCARAARYTHAA | ||
| RAAYYTKGGDTCWATWAAYCARGCHATGGTRACRAGRTGTGARCCAGTYGTBTGYTAYYT | ||
| VTATGGHAARAGRGGDGGRNGGRAARAGYYTRACWTCNAATTGCWTTGGCMANCMAAAAT | ||
| TTGYAAACAYNTATGGTGNTTGARCCWGARAARAATATHTAYACHAARCCTGTKGCYTCW | ||
| GATTAYTGGGATGGWTAYAGTGGRCAAYTRGTKTGYATYATTGATGAYATYGGYCAAAAY | ||
| ACAACWGATGARGAYTGGTCWGATTTTTGTCARTTRGTGTCWGGRTGYCCAATGAGRTTR | ||
| AAYATGGCYTCTYTKGARGARAAGGGYMGRCATTTTTCYTCWCCYTTYATAATWGCWACW | ||
| TCMAAYTGGTCWAATCCAAGTCCWAAAACAGTYTATGTKAARGAAGCHATWGAYCGYAGR | ||
| CTYCAYTTYAARGTTGARGTKAARCCYGCYTCATTYTTYAAAAATCCTCAYAATGATATG | ||
| TTRAATGTYARTYTRGCHAAAACWAATGATGCWATYAARGAYATGTCWTGTGTTGATYTR | ||
| RTWATGGATRGWCAYAATRTTTCAYTRWYKGAHTTRCTYAGTTCHYTRGTBATGACAGTT | ||
| GAWATTAGRAARCARAAYATGWSWGAATTYATGGARYTKTGGTCWCAGGGAWTNHTCAGA | ||
| TGATGAYAATGAYAGTGCAGTDGCYGARTTTTTCCARTCTTTTCCMTCTGGTGARCCATC | ||
| DRRYTCYARRTTRTCWVGBTTTTTCCAATCWGTYACYAAYCAYAARTGGGTTGCWGTKGG | ||
| RGCTGCWGTKGGHRTWCTYGGDGTKYTBGTKGGRGGDNTGGTWYGTSTAYAARCATTTYW | ||
| CHMRVARRSARGAAGARCCMATYCCARSTGAAGGRGTDTAYCATGGYGTRACHAARCCYA | ||
| ARCARGTRATYAAAYTRGATGCWGATCCWGTRGARTCNCARTCAACTYTRGNAAATWGCW | ||
| GGWYTRGTBAGRAARAAYYTKGTYCARTTYGGAGTTGGDGAGAARAATGGRTGTGTKAGA | ||
| TGGGTYATGAATGCYTTRGGARTKAARGATGATTGGYTRYTWGTDCCYTCYCATGCTTAY | ||
| AAATTTGARAARGATTATGAAATGATGGARTTTTATTTYAATAGAGGTGGWACTTAYTAY | ||
| TCAATYTCWGCWGGHAATGTTGTBATTCAATCTTTRGATGTKGGRTTYCARGATGTKGTT | ||
| YTRATGAARGTKCCYACAATTCCHAARTTTAGAGAYATWACHSARCATTTTATYAARAAR | ||
| RGDGATGTRCCTAGAGCYTTGAATMGBYTGGCAACAYTDGTRACAACHGTWAATGGRACY | ||
| CCWATGTTAATTTCWGAGGGHCCWYTVAARATGGARGARAARGCYACYTATGTTCAYAAR | ||
| AARAATGATGGWACHACHRTWGAYTTRACTGTDGAYCARGCMTGGAGRGGWAAAGGHGAR | ||
| GGTCTYCCWGGRATGTGYGGTGGSGCCYTRRTDWCWTCVAATCARTCYATMCARAATGCM | ||
| ATHTTRGGHATYCATGTTGCYGGWGGAAATTCAATTYTDGTKGCDAARTTRGTDACYCAA | ||
| GAAATGTTYCAAAAYATWGAYAAGAAAANTTGAAAGTCAGAGAATWATGAAAGTGGARTT | ||
| TACTCAGTGTTCAATGAATGTRGTCTCCAAAACGCTTTTTARAAAGAGYCCMATTYATCA | ||
| YCACATTGAYAAAAMCATGATTAATTTTCCTGCWGYKATGCCYTTTTCWARRGCWGAART | ||
| WGATCCMATGGCWRTRATGYTRTCHAARTATTCWYTWCCTATKGTDGAWGARCCAGAKGR | ||
| YTAYAARGADGYTTCWRTYTTTTWYCAAAAYAAAATWKTRGGYAAGRSTCMKYTRGTTGA | ||
| TGAYTTTYTRGATMTTGAWATGGCYATWACWGGGGCYCCWGGHATWGATGCHATYAAYAT | ||
| GGAYTCWTCYCCTGGRTWTCCTTATGTYCARGARARRTTRACYAAAAGAGATTTRATTTG | ||
| GYTKGAYGADAATGGWWTRYTKYTRGGDRTKCATCCWMGRYTGGCHCARAGAATYTTATT | ||
| YAAYACWRYHATGATGGAAAATTGTTCWGAYYTRGATGTTGTTTTYACWACYTGTCCMAA | ||
| RGATGARTTRAGACCWYTRGAVAAAGTKTTRGAATCWAAAACWAGRGCWATTGATKCTTG | ||
| YCCYYTKGAYTAYACAATTYTRTGYMGRATGTAYTGGGGTCCAGCYATTAGTTATTTYCA | ||
| YYTRAATCCWGGDTTYCAYACWGGTGTTGCWATWGGMATWGATCCTGAYARACARTGGGA | ||
| YSAAYTWTTYAAAACAATGATWAGATNTYGGRGATGTTGGTCTWGAYTTRGNAYTTYTCY | ||
| GCYTTTGATGCYAGTCTYAGTCCATTTATGATWAGRGARGCDGGWAGAATYMTSASTGAR | ||
| HTRTCTGGARCNCCWKYYCATTTTGGMRMRGCYCTYATYAAYACHATYATTTATTCYAAR | ||
| CAYYTRYTKTAYAAYTGTTGTTAYCAYGNTBTRTGGKTCAANTGCCHTCTGGGTCTCCTT | ||
| GYACAGCTTTGYTRAATTCAATTATHAAYAAYRTYAAYTTGTATTATGTKTTTTCYAARA | ||
| TWTTTRRAAAGTCTCCAGTTTTCTTTTGTSADGCYBTGARRATYCTYTGTTAYGGAGATG | ||
| ATGTYYTDATWGTYTTYTCYMGASAKGTYCARATTGAYAAYCTKGAYYYDATTGGACARA | ||
| RAATTGTDGATGAGTTYAARAARYTBGGHATGACAGCYACTTCWGCTGAYAARWMTGTDC | ||
| CBCARYTGAARCCAGTYTCDGARTTRACWTTTCTHAARAGRTCTTTYAATYTRGTDGARG | ||
| AYAGRATYAGRCCTGCWATTKCDGARAARACMATWTGGTCWTTRRTWGCHTGGCARAGAA | ||
| GYAAYGCTGARTTTGARCARAATYTRGARAAYGCYCAGTGGTTTGCTTTTATGCATGGHT | ||
| ATGARTTYTAYCARMAATTYTATYATTTTGTTCAGTCCTGYTTGGAGAAANNGARATGAT | ||
| AGAATAYAGRCTTAAATCWTATGATTGGTGGAGAATGARRTTTWNN |
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primerschemes/varvamp-hev3-ch1-m-i-uc-l/1000/v1.0.0/README.md
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| Original file line number | Diff line number | Diff line change |
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| # varvamp-hev3-ch1-m-i-uc-l 1000bp v1.0.0 | ||
|
|
||
| [primalscheme labs](https://labs.primalscheme.com/detail/varvamp-hev3-ch1-m-i-uc-l/1000/v1.0.0) | ||
|
|
||
| ## Description | ||
|
|
||
| Pan-specfic primer scheme for HEV genotype 3 ch1, m, i, uc, l designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates. | ||
|
|
||
| ## Overviews | ||
|
|
||
|  | ||
|
|
||
| ## Details | ||
|
|
||
| ```json | ||
| { | ||
| "ampliconsize": 1000, | ||
| "schemeversion": "v1.0.0", | ||
| "schemename": "varvamp-hev3-ch1-m-i-uc-l", | ||
| "primer_bed_md5": "60db2382ac7114153c6bc93acdb5f70d", | ||
| "reference_fasta_md5": "cb7e70c64382a1a8434ab3923a6265c9", | ||
| "status": "validated", | ||
| "citations": [], | ||
| "authors": [ | ||
| "Jonas Fuchs" | ||
| ], | ||
| "algorithmversion": "varVAMP:0.8.2", | ||
| "species": [ | ||
| 291484 | ||
| ], | ||
| "license": "CC BY-SA 4.0", | ||
| "primerclass": "primerschemes", | ||
| "infoschema": "v2.0.0", | ||
| "articbedversion": "v2.0", | ||
| "collections": [ | ||
| "CLINICAL-ISOLATES", | ||
| "COMMUNITY", | ||
| "WHOLE-GENOME" | ||
| ], | ||
| "links": { | ||
| "protocols": [], | ||
| "validation": [ | ||
| "https://www.biorxiv.org/content/10.1101/2024.05.08.593102v1.full" | ||
| ], | ||
| "homepage": [ | ||
| "https://github.com/jonas-fuchs/ViralPrimerSchemes/tree/main/varvamp_tiled/HEV_2" | ||
| ], | ||
| "vendors": [], | ||
| "misc": [] | ||
| }, | ||
| "description": "Pan-specfic primer scheme for HEV genotype 3 ch1, m, i, uc, l designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates.", | ||
| "derivedfrom": null, | ||
| "contactinfo": "[email protected]" | ||
| } | ||
| ``` | ||
|
|
||
|
|
||
|
|
||
| ------------------------------------------------------------------------ | ||
|
|
||
| This work is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/) | ||
|
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|  |
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primerschemes/varvamp-hev3-ch1-m-i-uc-l/1000/v1.0.0/info.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| { | ||
| "ampliconsize": 1000, | ||
| "schemeversion": "v1.0.0", | ||
| "schemename": "varvamp-hev3-ch1-m-i-uc-l", | ||
| "primer_bed_md5": "60db2382ac7114153c6bc93acdb5f70d", | ||
| "reference_fasta_md5": "cb7e70c64382a1a8434ab3923a6265c9", | ||
| "status": "validated", | ||
| "citations": [], | ||
| "authors": [ | ||
| "Jonas Fuchs" | ||
| ], | ||
| "algorithmversion": "varVAMP:0.8.2", | ||
| "species": [ | ||
| 291484 | ||
| ], | ||
| "license": "CC BY-SA 4.0", | ||
| "primerclass": "primerschemes", | ||
| "infoschema": "v2.0.0", | ||
| "articbedversion": "v2.0", | ||
| "collections": [ | ||
| "CLINICAL-ISOLATES", | ||
| "COMMUNITY", | ||
| "WHOLE-GENOME" | ||
| ], | ||
| "links": { | ||
| "protocols": [], | ||
| "validation": [ | ||
| "https://www.biorxiv.org/content/10.1101/2024.05.08.593102v1.full" | ||
| ], | ||
| "homepage": [ | ||
| "https://github.com/jonas-fuchs/ViralPrimerSchemes/tree/main/varvamp_tiled/HEV_2" | ||
| ], | ||
| "vendors": [], | ||
| "misc": [] | ||
| }, | ||
| "description": "Pan-specfic primer scheme for HEV genotype 3 ch1, m, i, uc, l designed with varVAMP on the basis of full length genomes. The design utilizes degenerated primers and was validated on clinical samples and isolates.", | ||
| "derivedfrom": null, | ||
| "contactinfo": "[email protected]" | ||
| } |
12 changes: 12 additions & 0 deletions
12
primerschemes/varvamp-hev3-ch1-m-i-uc-l/1000/v1.0.0/primer.bed
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| ambiguous_consensus 25 47 hev3ch1miucl_0_LEFT_1 0 + AGGCTCCTGGCATYACTACTGC | ||
| ambiguous_consensus 1422 1442 hev3ch1miucl_0_RIGHT_1 0 - TCCTGYCCYARCCACTTCAT | ||
| ambiguous_consensus 2514 2534 hev3ch1miucl_1_LEFT_1 0 + TAYCARCGYTACCCYGAGTC | ||
| ambiguous_consensus 3899 3921 hev3ch1miucl_1_RIGHT_1 0 - CCGTGAGYTCRAARACCARCAC | ||
| ambiguous_consensus 4804 4825 hev3ch1miucl_2_LEFT_1 0 + YGGGYTGTATGCYGGYGTGGT | ||
| ambiguous_consensus 5965 5986 hev3ch1miucl_2_RIGHT_1 0 - ARGTRGCCTCCTCYTCRGCCA | ||
| ambiguous_consensus 1299 1319 hev3ch1miucl_3_LEFT_1 1 + CAGTGYCGCCGYTGGYTATC | ||
| ambiguous_consensus 2644 2665 hev3ch1miucl_3_RIGHT_1 1 - GRTAYGCYGCCTCRAGCCTCT | ||
| ambiguous_consensus 3570 3591 hev3ch1miucl_4_LEFT_1 1 + CACTYACCCGYCAYACAGAGA | ||
| ambiguous_consensus 4958 4980 hev3ch1miucl_4_RIGHT_1 1 - CACAHACCTGCGCMACATTCGT | ||
| ambiguous_consensus 5752 5771 hev3ch1miucl_5_LEFT_1 1 + GSCCRYTGGTGCCDAATGC | ||
| ambiguous_consensus 7075 7094 hev3ch1miucl_5_RIGHT_1 1 - TGRAARGCRCAHCCCTGCA |
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