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Example searches
- Gene containing a mismatch and a frameshift
- Gene spread on several contigs and containing a gap
- Gene with a 5' exon just encoding a methionine
Expert searches
- Parameters to account for additional/missing bases in predicted exons
- Parameters to identify divergent exons and very short exons
- Parameters to account for low homology at intron borders
| Gene containing a mismatch and a frameshift | Back to top |
| Organism | Fusarium oxysporum f. sp. lycopersici 4287 |
| Genome file |  supercontigs v 1.0.0 |
 Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MALVIPYTYIQCPCSDQSPPDLPQARQSQSSDERTFDPRDPRSNYSLYPLEYLLYCEDCQ QIRCPRCVNEEVVTYYCPNCLFEVPSSNLRSDGNRCTRSCYQCPVCIGPLQVMETPIEKD QSHLGADIPGPQYALYCQYCNWTSTEIGIKFDKPNGIHSQLSKINNGGDLKLTAKELKER RKENPDEPPLADSDVDTDLQYANLKSFYQSQLADTNAASSGISPLNDTTGYGSPAASLSR IMAMYTGHGHARKRNGPSEVMREALSAEEGLKLADLDESAQIKKLHQEGWDATATIQQNL EQAEVQRFQDGLRPIPHLLRTKRSKRCSVCRHIISKPENKVTSTRFKIRLVAKSYIPTIT IKPLNPTAGTVPTTQRPQILEERPLKPLTPHHYIITFKNPLFDGIKVTLATPNSTPGRFS SKVTILCPQFDIDANTDMWDDALKDDDRDKKRKGEESSGQPEAGKIWERGRNWVSIILEV VPASLRLDGQKDKSPLKEDEDILEIPMFVRMEWEPDSQQDVGAASAKEKDAQERRELAYW CVLGVGRISHD |
| Search parameters | standard parameters |
| Result |
|
| Resultfile | ScipioResult_Fusarium_oxysporum.yaml |
| Gene spread on several contigs and containing a gap | Back to top |
Query sequence derived from cDNA.
| Organism | Bombyx mori str. Dazao |
| Genome file | supercontigs v 1.0.0 |
| Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MEHSLQHRERVGVQDFVLLEDYRSEAAFIDNLKKRFHENIIYTYIGNVLISVNPYKNLPI YTEEKTKLYFKKAFFEAPPHVFAIADNAYRSLVYEHREQCILISGESGSGKTEASKKVLE YIAARTNHLRNVENVKDKLLQSNPLLEAFGNAKTHRNDNSSRFGKYMDIQFNYEGGPEGG HILNYLLEKSRVVSQMHGERNFHIFYQLLASSDQSLMTHLKLQGRPEAYKYTSDSTSHMS QRANDQEQFRVVQEAMKVIEIGESEQREIFEIVASVLHLGNVKFVQNDKGYAEILSHDAN SGNAADLLKVNATALREALTNRTIEARGDVVSTPLDVEQAQYARDALAKAIYDKHFSWLV SRLNSSLAPIEKDAKSSVIGILDIYGFEIFPKNSFEQFCINFCNEKLQQLFIQLTLRQEQ EEYLREGIEWEPVEYFNNIIICDLIEARHKGIISILDDECLRPGDATDASFLDKLNQHLD GHQHYKSHRKSDTKTQKLMGRDEFCLVHYAGEVTYNVNTFLEKNNDLLFRDIQSLMASSD NTIVGCCFKVTFSNREPSYIRCIKPNDFKAPMQFDDKLVSHQVKYLGLMENLRVRRAGFA YRRTYEAFLERYKCLSAETWPNYRGAARDGVQRLVEALQYEKEEYRMGNTKIFVRFPKTL FATEDAFQIKKNDIATIIQSRWRGYYLRKRYLRMRNAAIVIQKWVRRFLAQRLRERRRKA ADVIRAFIKGFITRNGPETPENRRFLGVAKVHWLKRLSAQLPTKLLDLSWPPCPSTCREA SEELHRLHRAHLARKYRLALSPDDKKQFELKVLAEKIFKYSCEAVKYDRRGYKARARGLL ASRAALYVLDAGGRRTFRLKHRLPLDRLTVVVTNESDSLLLVKVPRDLKKDKGDLIISVT HLIEALTIVTDYTKKPELIEIVDTRTIAHSLVNGKQGGTIEVTKGTQPAIQRAKSGNLLV VATP |
| Search parameters | standard parameters |
| Result |
|
| Resultfile | ScipioResult_Bombyx_mori.yaml |
| Gene with a 5' exon just encoding a methionine | Back to top |
| Organism | Magnaporthe grisea 70-15 |
| Genome file |  supercontigs v 6.0.0 |
| Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MGITRRGKDKAAAGQAVAGGASGGRARPKKATFETSKKKDVGVSDLTLLSKVSNEAINEN LQKRFEGREIYTYIGHVLVSVNPFRDLGIYTDQVLDSYKGKNRLEMPPHVFAIAESAYYN MKAYKDNQCVIISGESGAGKTEAAKRIMQYIASVSGGDSTDIQQIKDMVLATNPLLESFG NAKTLRNNNSSRFGKYLQIHFNSVGEPVGADITNYLLEKSRVVGQITNERNFHIFYQFTK GASEHYRQMFGIQKPETYIYTSRSKCLDVDGIDDLAEFQDTLNAMKVIGLSQEEQDSVFR ILAAILWTGNLVFREDDEGYAAVTDQSVVEFLAYLLEVDPQQLIKAITIRILTPRSGEVI ESPANVAQAMATRDALAKSLYNNLFDWIVERINQSLKARQPTSNSVGILDIYGFEIFEKN SFEQLCINYVNEKLQQIFIQLTLKAEQDEYAREQIKWTPIKYFDNKIVCDLIESVRPPGV FSALKDATKTAHADPAACDRTFMQSVNGMSNAHLIPRQGSFIIKHYAGDVAYTVDGITDK NKDQLLKGLLGMFQVSQNPFLHTLFPNQVDQDNRKQPPTAGDRIRTSANALVETLMKCQP SYIRTIKPNENKSPTEYNVPNVLHQIKYLGLQENVRIRRAGFAYRQSFEKFVDRFFLLSP ATSYAGEYTWQGSYEAAVKQILKDTSIPQEEWQMGVTKAFIKSPETLFALEHMRDRYWHN MATRIQRMWRAYLAYRAESATRIQTFWRKKRTGAEYLQLRDHGHRVLQGRKERRRMSILG SRRFIGDYLGINASSGPGAHIRNAIGIGSNEKTVFSCRGEILEAKFGRSSKASPRILIVT NSKFYVVAQMLVNGQVQITAEKAIPLGAIKFIGASSSRDDWFSLGVGSPQEADPLLNCVL KTEMFTQMERVMPGGFNLKIGDSIEYAKKPGKMQVVKVLKDSPNPVDFYKSGAVHTQQGE PPNSVSRPTPKGKPVPPRPITRGKLIRPGGPNGRPARGTTNRTPQPRPGGASASAVASRP VPQAQPQAQAQVAASIPVRTQQQSQTSSASVRAPPPPPPAAPPAKAKIMAKVLYDFAGQK ENEMSIKEGDLIEIVQKENNGWWLAKSGNQQAWVPAAYVEEQKQAPPPVAASRPPPPAPP AANGKNKPLPPAKRPAAGKKPASLQPRDSGMSLNGSDGSRSNTPTPSLGNSLADALLARK QAMAKKDDDDDW |
| Search parameters | standard parameters |
| Result |
|
| Resultfile | ScipioResult_Magnaporthe_grisea.yaml |
| Parameters to account for additional/missing bases in predicted exons | Back to top |
| Organism | Phytophthora sojae P6497 |
| Genome file |  supercontigs v 2.0.0 |
| Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MTSEGDVVDDVCVRYACKCGHLAPVSSLFYSETCEKLVCRLPGCSVEEFESYYCGNLLVNLPSKEASM YQNRSSRCFSCPTCENALSTAFHENEQRFFFLCAHCRWESLSVGLADDDPDALVMTAITRERQAAHED IFQALHSHYSTLSSSPANGGAAGVLSASSGAPFGRSSSLQLLADSMKELQREHQMKKFRLQRMAEMGG WKYDQALAKVEEKERWLMEQRREHQWPELSMQLAALSKQGTSYGEESPEKTREVLRNLSQKCDMGEVS TLHQRLLNPLDQAREADQLFPSRPLLRVKRTWRCVESIERGTAGILVKPQISPMSGDSSLPVSASWFK KANLAAQYVPVVTFQRLPYRVGEGGGVECILLVENPLDDAIRITFHSTPTASEDSNENGYVDFQDLTP IIVGPYEDPNLADAFIDDEPPFGANGDEHNTMLLQATRNLIKIKLPLSVNAATTIPISTLSARFIMDT EKFDEDANEVIENSLLSVPVVITAPIIKIGD |
| Search parameters | Min. Score = 0.2; Min. Identity = 60%; Max. Mismatch = "∞"; Gap to Close = 15 aa; Min. Intron Length = 34 na |
| Result |
|
| Resultfile | ScipioResult_Phytophthora_sojae.yaml |
| Parameters to identify divergent exons and very short exons | Back to top |
| Organism | Homo sapiens |
| Genome file | chromosome_assembly1 v 1.0.0 |
| Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAFAQELEELTSTSVEHIIVNPNAAYD KFKDKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTT EVEKIKTTVKESATEEKLTPVLLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAK RLLLQLEATKNSKGGSGGKTTGTPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELE TAVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAK HKASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDT TQQMIANSLKDNTTLLTQVQTTMRENLATVEGNFASIDERMKKLGK |
| Search parameters | Exhaust Align Size = 15000 bp |
| Result |
|
| Resultfile | ScipioResult_Homo_sapiens.yaml |
| Parameters to account for low homology at intron borders | Back to top |
| Organism | Thielavia heterothallica ATCC 42464 |
| Genome file | supercontigs v 1.0.0 |
| Genomic DNA subsequence (useful for command-line tests of Scipio) | |
| Query sequence | MSSHKAIVSSFVEGAPPGELSDVVADIKALTISSPGLVNELGPAFQKYNEEQFTTVKLPG GSQPVIISSHSALGNGRYYDLESSCSFAFDHITQKASAVESYVPEGDGVDLAKSILKGLS TYVNEHFTNAAYGAYPIENGSKIAIIIVANKYSPNNFWNGRWRSLYIFNPASSALEGSIK VDVHYYEDGNVRLLTNKSATATVPSGTGAAIAKEISAGERKYQEELNRSFTSLSEGAFKA LRRQLPVTRQKIEWDKVASYRLGQDIGGGSSRR |
| Search parameters | Max. Move Exon = 6 aa |
| Result |
|
| Resultfile | ScipioResult_Thielavia_heterothallica.yaml |
