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Snail DNA Sequencing: Improving Data Quality and Identity

This PowerPoint presentation discusses sequence editing, data quality control, and identity improvement of snail DNA through techniques like Illumina sequencing and BLAST analysis.

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Snail DNA Sequencing: Improving Data Quality and Identity

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  1. Today • HK • *.ppt • Sequence editing, Chromas • Illumina sequencing • MBF visit/ GALAXY data QC • Sequence editing and BLAST data quality, improve, identity of snails

  2. SNAILAND PARASITES BIOLOGY DNA “identity, possibilities” phylogenetics CTAB/DNAzol CTAB/DNAzol Illumina (full) genome sequencing gel electrophoresis nanodrop spec PCRrDNA/mito Qubit Fluorometry Covaris fragmentation Ampure (fragment collection) Kapa DNA library preparation kit Pippin size selection QC Bioanalyzer, Qubit, qPCR Illumina run TA cloning, B/W screening electrophoresis Qiagen plasmid extraction Restriction digests direct sequencing M13 sequencing Sequence ID (BLAST) editing Galaxy QC Data file (MT) genome assembly Mitos, manual annotation Gene annotation Primer design, walking Phylogenetics GenBank submission

  3. *.ppt

  4. DNA SANGER SEQUENCING >12-6_CR NNNNNNNNNNNNNNNNAGNNNNNNNNCNCNNNCCCNNNNNNNCNNNNAAC NNNNNNNNNNNAGNTTCNNNNNNNNNNNNNNNNNNNNNNNNNGNNNNNNN NGANNANANANAANNANNNNNNNNNNNGNNNCTNANANNGNNNNNNNNAA TNANTNNNNNCNNNCNNNNNTNANTCCTGGNNCANNTATGTTTANNNNNN TTNNAANNNANTTNANTNNNNCTATNNNTGAANNNNNNNCNGNTNNNTGN NGANNNNNNATNNNNNGGNCCACCNAANTNCCNNANNGNNNNGTTGAANT TGATAGGNGAGGANATACNGNTNNACCCGNTNCNACTCCCCCTTCNNTTN NNGAGCTNNNGANTNNNAATACNAANNANANGGGGGNNAANNCNAAANNN NNTANNNTNTNNNCNAGGAAACTNNTNNCNGGNGAGCCNATANNNNNNGN ANCNTTCNNTTNNNNNNCCCCNNNNNAANNANGNNTTACNNTNAAAAAAA NNNNNNNAANNNNNGNGNGGNNNNANNNNNNTNGTAANNNNNNNNTNCNN NNNNNNNNNNANNNNNNNNNNNNNNAGNNNANNNAANNGNNNNNNNGGNT NNNNNNNNNNNNNNNNNNNNNNNAANNNAANNNNNNNNNNNNNNNNNNNN NNNNTNNNNNNNNNN >01-1_16F NNNNNNNNNNNNNATTATNGNCNANNTCTTCTGCCCGGNGTTTNTNNNNN NGCCGCAGTACCTTGANNNNNNNNNNNNNNNNNNNNTNNNNNNNNGNNNN NNNNNNNNNNNNNNANTAGTAACTATAATAAGAAATTTTATTTTAACTTA ATGAACTGGTGAAAATACCAGTATATAGAANNNNNNNNNNAANACCCTTA GAGTTTTTAAATAAAGATTGTTTAAGACTTTGATGTACCATCATCTTAAA GTACATTATACAAAACACTTTTTTGNTGGGGCGACAAGAAAGCNATATAA CCTTTCTATTTACNCTAAAAGTGGGTATTANANCTGACNATATTATTATG AATGACTAAACTACCTGAGGGANAACNGCATANTGATNAATANTANTTNG NGANCTCGANGTTGGACTAGGNACTNGNACNCTANCCNNGANAAAANNTN NNNNNNNNANANAANCCCNANNNGNNCTGANNNNNNNNNNNNNNANGGGG NNNAAANNNNNNCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNN >02-1_CF NNNNNNNNNNTNNGGGNNCNNGNGTGGCTTGGTCGGNNNAGGNNNNNNNN GNNNNTCGTTTGGAANTNNNNNNNNNNNNNNNNNNGNNTNNNNATTTTTA TAATNNANNNNNNNNNNNNNTTTTGTAATGNATTTTTTTTATAGTTATAC CTATAATAATTGGAGGCTTTGGGAATTGAATAGTACNTTTNNNNNANNGG NGCTCCCGATATAAGCTTTCCTCGAATAAATAATATANNANNNNGANNAN NACCCCCTTCATTTATCTTATTATTATGTAGGTCTATAGTTGAGGGTGGG GNNNNAACNNNTTNANNNNNTNNNNNCCCNCNCTCAANNNNNGNNNNNNN NNNNNNNNNNANANNNNANGGGGGNNNNNTCNAANNNNNNNNNNNNNNNN NNNNNAAANNTTANNNNNGNNNNNCNNNTNNNNNNNGNNNNNNNNAANNN NNNNNNNNNNNNNNNNNNNNNNNAANNNNNAAAAANNNNNNNNNNNNNNN NGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNN NNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNANNNNNNNNNNNNNNNNNNNNTNNNNNNTNNNNNNNNN >03-2_16R NNNNNNNNNNNNNNNAGCTTTNATCACGGTTAGTGTANAAGTCCCNNNNN NAACATCGAGGTCACAAANNNNNNNNNNNNNNNNNNNGNNANNNNNNAGG TAGTTTAGTCATTNNNNNNNNNNNNNNCNGATCTAATACCCACTTTTAGC GTAAATAGAAAGGTTATATTGCTTTCTTGTCGCCCCAACAAAAANNNNNN NNNNATAATGTACTTTAAGATGATGGTACATCAAAGTCTTAAACAANNNN NATTTAAAAACTCTAAGGGTCTTCTCGTCTTTTTTCTATATACTGGTATT TTCACCAGTTCATTAAGTTAAAATAAAATTTCTTATTATAGTTACTATTC ATTACTTCATTCATACTAGACTACAATTAATAGCCAATTGATTATGCTAC CTTAGCACAGTCAAGGTACTGCGGCCGTTTATTATAAACACCGGGCAGAA GATATCGACAATAATAATAATTTAGTTCATCTGCCGACTATGTTTNNNNN NANCNGGGNGGNNNNNNNGGGGGGGGGGGNNANNNANNNNNNANTTCANT TTNNTGGANGTTGANNNANANNNNNCGNACCNNNCNTTNNCNGGTTNNNG NGGGNCNGAACTTTACCNNNNGNAATTTNNNNGNANNNNGGACGNTNNGG NNNNNNNNNCTGTTNNNNNN >04-2_CR NNNNNNNNNNNNNNNNNNNNNNNNNNTCCTCTTGGNTCNNGANNNNNNNT TAAAATTTNGATNAGGTNNNNNNNNNNNNNNNCCNGNNNNNNNAGGNNAT GANAATAATANNNNNNNNNNNNNNNNTAACACTGATCAAACAAATAAGCT TATTCGTTCCAGTGTAATACCAGGAGAACGTATATTAAAAATTGTNNNNA TAAAATTAATAGCACCTAAAATAGATGATAACCCAGCTAAGTGTAATGAG AAAATAGCCAAATCTACTGATGAACCAGAGTGAGCTACAGGTCCTGATAG TGGGGGATAAACAGTTCACCCAGTTCCAACCCCACCCTCAACTATAGACC TACATAATAATAAGATAAATGAAGGGGGTAATAGTCAAAATCTTATATTA TTTATTCGAGGAAAGCTTATATCGGGAGCACCAATTAATATNGGTACTAT TCAATTCCCAAAGCNTCCAATTATTATAGGTATAACTATAAAAAAAATCA TTACAAAAGCATGTGCTGNNNNGATTACATTATAAAAATGNTCATCCANT AGTANNNNNGATGNTNCTAATTCNAAACGAATTAACAAGCTTANGCCTGT ACCGANCNAGCNNNNNNCNNATNCCNAAAANTAANNNTNANGNACCANNN NTCTTTNNTGATTNGGTNNNNNNN >05-3_CF NNNNNNNNNNNNNNNNNATTNTGCNCNGCGTANNTTATTANCGGNNNNNN NNNNNNNACTGTGCTAAGGTAGNNNNNNNNNNNNNNNNNNNTGNANNNNN GAATGAAAGGACTAATAGNNNNNNNNNNNNNNNNNANNCTATTATTTTGA ATTTATTTATTAAGTGAAAATACTTATACAAAGAAAAAAGACGAGAAGAN NNNNTNNNNATTTTAATAAAATATTTAATAATTTTTTTTTGTTGGGGCGA CATTGAAACAATTAAACTTTCATTAACAATCAAGACATTTAGGTTTGAAA GAATAAATTACCTTAGGGATAACAGCATAATTAATTATTTAGTTTGTGAC CTCGATGTTGGACTAGGAACTAGAAGATTAACCGTCTAAATAGATTGNNN NGTTCGAACAGAAATTCCTACGTGATCTGAGTTCNGANNGGG >06-3_16F NNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNTNAANNNNNNNNNNNNNNNNNNNNGNNNNNNTNNNNATAGTTATA CCAATAATAATTGGAGGGTTTGGAAATTGAATAGNNNNNNNNNNNNNNNN NNNNNNNNCCAGATATAAGATTTCCTCGTATAAATAATATAAGANNNNNN NNNNNTACCACCTTCGTTTATTCTCTTACTTTGCTCTAGAANAGNAGAAG GTGGGGTAGGTACTGGATGAACAGTTTACCCACCATTGAGTGGACCTATT GCTCATGGTGGATCTTCTGTTGATTTAGCTATTTTTTCTTTACATTTAGC CGGTTTATCCAGGATTTTAGGAGCAATTAATTTTATTACTACNATTTTTA ATATACGATNNNTNTNNNNNACATTANAACNAATAANATTATTNGATGAT CTGNATTAGNNNGNGGGGGGGNGNNNNTCTTTNANCCNNNACCNGTACTT GCANGGGNNNATTACNATGNTTTTAACNNANCNAATTTTAATACCACTTT TTTTTGATCNNGCTGNAGTGNGANCNNNTTTTNTTNTCANNNTTNATTCN NATTTTTTTNNTCNNNCCGNNNNNTNAA >07-4_16R GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNTNNANNNNNNTNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNN >08-4_CR NNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTCCNGCAGGANNNNNNNNNN NNNNTTAAAATTTCGATCTGNNNNNNNNNNNNNNNNNCCNGNNNNNNNTG GTAAAGATAAAAGAANNNNNNNNNNNNNNTAATACAGATCATACAAATAA TCTTATTCGTTCTAATGTAATACCTGGAGATCGTATATTANANNNNNNNN NNNAATAAAATTAATTGCTCCTAAAATCCTGGATAAACCGGCTAAATGTA AAGAAAAAATAGCTAAATCAACAGAAGATCCACCATGAGCAATAGGTCCA CTCAATGGTGGGTAAACTGTTCATCCAGTACCTACCCCACCTTCTACTAT TCTAGAGCAAAGTAAGAGAATAAACGAAGGTGGTAGTAATCAAAATCTTA TATTATTTATACNANGAAATCTTATATCTGGNGCANCAATGANAAGTGNA ACTATTCANTTTCNAAACCNNNCANTNATNNTTGGTATAACNATGAAAAA AATNNTAACNAANNNNNNGAGCNGNANNNNNNNCNTTNNNNAAAANGNTC GNCAATNNAANNNNNNNNNNNNNNCNNNNTNNAANNAANNNNNNNNNNNA NNCNNNNNNNNNNANCNNNNNNNNNNNNCNAAANNNNNNNNNANGNNCNN NNNNNTNNNNNATTNNNNNNNNN >09-5_16F NNNNNNNNNGNATTTTCTGCNCGGNNTTTTTTAATTAACGGNNNNNNTAC CTTNNCTGTGCTAAGNNNNNNNNNNNNNNNNNATNAATTGTAGTCTAGTA TGAAAGGNNANNNNNNNANNNCCTATAACATTTAGTTTTAGTTGAATTTA CTTATCTGGTGAAAATGCCAGTGATAAGAAAAAAGACGAGAANACCCTTA GAGTTATTAAATATATCTGTTATTATATAATATTAAAACAGCTATTTGTT TGTTGGGGCGACAAGAAAACAAGTTTAACTTTTCTACTTAATTAATTTTA TGTGCCGAAAAATATTAAGGATAATAAACTACCTTAGGGATAACAGCATA ATGATATAATTTAGTTTGTGACCTCGATGTTGGACTAGGAACTTGAACAC TAACAGTGCTTAAAGATTGTTCTGTTCGAACATATAACTCCTACGTGATC TGAGTTCAGACCGG >10-5_CF NNNNNNNNNTNNNNNNNNNNNNNNNGGNNTGNNNNANNNNNNCNNNNNNT NATTNNNNNTGANNNNNNNNNNNNNNNNNNNNNGGANGANANNNTTANAN NNTANNNNNNNNNNNNNNGCNNNTNNNNNNNNTTTNNNTANAANTANNCC NNNNNNTNNNNNNNNNNNNNNANNNNNNGGNNNNNNNNNNNNNNNNNNCG CCNGANANAANNNNNNNCNNNNANNNAANATANNNNATTNNNNNNNNNNN CCNNCNNTCNATTACNNNNNNNNNNNNNGANAATTNANNNNNNNNNNNAA NNNGNNNANNNNATNNCCNCCNTCNNNNAACNTNNCNNTGNNNNNNNNNT GNANNNNNNNATTTNNCNTANTNNNNNNNNGNNNNNNNNNNNNGGNNNNA NNTNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGNAANNNNNNNNTNNNNN NNTNNNNNNNNNNNNNNNNGGGGGGNNNNNNNNNNNNTTCNNNNNNNNNG GGNNNNNNNNNNNNANNNNNNANNNNNNNNNNNNTNNNCNNNNNNGNGNN NNNNNNNNNNNNNNNTNNNNTNTNNNNNNNNNNNNNNNAA >11-6_16R NNNNNNNNNNNNNACATCTTTAGCNCTGTTAGTGTTNAAGTTCNNNNNNC AACNTCGAGGTCACAAACNNANNNNNNNNNNNNNGNTATNNNNAAGGNAG TTTATTATCCNNNNNNNNNNNNNNGNACATAAAATTAATTAAGTAGAAAA GTTAAACTTGTTTTCTTGTCGCCCCAACAAACAAATAGCTGTNNNNNNNN NNTATAATAACAGATATATTTAATAACTCTAAGGGTCTTCTCGTCTTTTT TCTTATCACTGGCATTTTCACCAGATAAGTAAATTCAACTAAAACTAAAT GTTATAGGTAGTATTCATTTATCCTTTCNTACTANACTACAATTAATAGC CAATTGATTATGCTACCTTAGCACAGTCNNGNACNGCGNNCGNTANNTNA AAAACNNNNGGNNNAANANNNNNNNNATATTTANGNNNNTATNNNNNNNN NTTTTNAANNNNNNNNGGNNNNN >13-7_16F NNNNNNNNNNNNNNNNNNNNNNTGCNNNNNNNNNNNNNNNNNNNNNGNCG CAGNNNNNTTNANNNNNNNNNNNNNNNNNNNNNNNNNNGNAGTCTAGNNN NNNNNNNNNNNNNNNNNTATNNNNGAAATTTTATTTTAACTTNNTGAACT GGTGNAAATACCNGTATATAGAANNNNNNNNNNNAAGACNCTTANAGTTT TTAAATAAAGATTGTTTAAGACTTTGATGTANCATCNTCTTAAAGTACAT TATACAAAACACTTTTTTGTTGGGGCGACAAGAAAGCAATATNACCTTTC TATTTACGCTAAAAGTGGGTATTANATCTGACNATATTATTATGAATGAC TAAACTACCTGAGGGATAACAGCATAATGATAAATATTANTTTGTGACCT CGATGTTGGACTAGGGACTTGTACACTAACCGTGATAAAAGCTTGTTCTG TTCGNACAATANACCCCTACGNGATCTNNNNNNNNCCNGNNNNNNNGNNG ANNGCAAAAGCTTGCCTGACTGTNNNNTGATAAGCCGANGCAGAAACNAA AGTTGGCTTTAATGATCCGGTGGCCTTGCGTGGAAGAGCCATCGCTNNAC AAATAAANNNACNGNNNNNTNACANGCTNATGGTGTCTGANANTTCACAT CNACNACNCCGNTTNGNACCTCNATGNNNNTNNNNNCNNCCTGGGGNTGA NNANNNNNNCNANGGNTNGNNNNCNCCNNTAAANNGGTNNNNNNNNCTGN NTTNANNNNNGGAAA >14-7_CF NNNNNNNNNTTTNGNNNNCTGGNGTGGCTTGGTCGGTACAGGNTNNNNNN TGTTNNTTCGTTTGGAATTNGNNNNNNNNNNNNNNNNNTGGATGAACATT TTTATAATGTAANNCNNCTNTNNNNNNNNNNTTTTGTAATGATTTTTTTT ATAGTTATACCTATAATAATTGGAGGCTTTGGGAATTGAATAGTACCTAT ATTAATTGGTGCTCCCGATATAAGCTTTCCTCGAATAAATAATATAAGAT TTTGACTATTACCCCCTTCATTTATCTTATTATTATGTAGGTCTATAGTT GAGGGTGGGGTTGGAACTGGGTGAACTGTTTATCCCCCACTATCAGGACC TGTAGCTCACTCTGGTTCATCAGTAGATTTGGCTATTTTCTCATTACACT TAGCTGGGTTATCATCNATTTTAGGNGCTATNNATTTTATTACTACAATT TTTAATATACGTTNNNCCNGGTATNACNCTGGAACNNATAAGCTNATTTG TTTGATCANNNNNNNNNNNNNNGNNNNNNTTNNTNATNATTGNCATTGNC NGNTTTTANNNGGGGGNNNNNACNNNTNNNNNTTAANNNGATCNNANNTT NNNNCTANGNTNNTTNGNTCNNNNNNNNNNNGGGGNNNNNCNNNTNNNNN NNNNNNNNNNNNNTTTNNNNTTTTTNNGGNCNCNNNNNNNNNNTNNNN >15-8_16R NNNNN >16-8_CR NNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNATANNCTTATTCNNNNNNNNGNNNNN NNNNNNNNANNNNNNTTANNNNNNNNNNNNNNNNATTANTANCACCTNNN NTNNNNNNNNNNNNNGGGGGGGNNGNNNGAAACAANNNNTNTTNNNNNAN NNNNNN >17-9_16CF NNNNNNNNNNNNNNGNNNANNNNNNNNNNGNNNNNGNNNNNNNNNNNNNN NNCNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNGNNNAGNNNNNNNNNG AANNNNNNNNNNNNNNNNNNNNNNNNNNNATNNNNNNNNNANNNNNACCN NNAANNNNTNNNNGGNNNNNAAANTANNNANNNACNCTTCNNATTNNNGC TNCNNATNNAANATTTCCTCNTNNNNNNANNANNNNNNNNNANNANNACN NNCNTNNNNNNNNNNNNNNNTTNGGTCTAAAAAANANANNGNNNNGGNGN NACNGGATNANCANTTNNNCNNCNTTGANNGNANCTTTGNNNNNNNNNAN NNNNNNNNNTNNNNNNNNTNNNNTNNNNNNNNNNNNNNNNNNNNNNNTTN NNNNNNNNNNNNNTNNCNCANNNNNNNNNNNNNNCNGGNNNNCNNNNNNN NNNNNNNNNNNNNNNNNNNCNNNTANTNNNNNTNTNNNNNTTTNNNNTNN NNNNNNNNNGGGCANNNNNNGNNTNANNNNNANNTNNNNNNNTTTTNNNC NNNNNNNGGGNNNNNNNTTNNNNNNNTNNNNNNNTTTNNNNNCNNNNNNN AN >18-10_16R NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTNNNNNNNNTTTTGTTGGGG NNNNNNGGNNNNNNNAANCTTTCATTANNNNNNNNACATTNAGGTTTGAA ANAATAAATNNNNNNNNGNANANNNNCANNNNNAATTATTNGNTNGNNAN NNCATNNNAGANTAGGANCNNGANNAAAANNNNNCNNNNNNAANGNTNNN NNAAAAANNTNCNAANGNTNTNANAANNCGNAANANAAANNTTATTTTTT TTNTTNGGNNNNNCANNNNNNNNNNGGGGNGCNNNTNNGNGGGGGGGAAA AAAACACTTTTTNTNNNNGGGGGGGGG >19-10_CR NNNNNNNNNNNNNANAGNNNNNNNNCCTCNNNCANGNNNNANNNNNNNNN NNAAAATTTCGATCTGNNNNNNNNNNNNNNNNCNNGCNNNNNNNGGNAAA GATAAAAGANNNNNNNNNNNNNNNNCTAATACAGATCATACAAATAATCT TATTCGTTCTAATGTAATACCTGGAGATCGTATATTAAAAATTNTNNNNA TAAAATTAATTGCTCCTAAAATCCTGGATAAACCGGCTAAATGTAAAGAA AAAATAGCTAAATCAACAGAAGATCCACCATGAGCAATAGGTCCACTCAA TGGTGGGTAAACTGTTCATCCAGTACCTACCCCACCTTCTACTATTCTAG AGCAAAGTAAGAGAATAAACGAAGGTGGTAGTAATCAAAATCTTATATTA TTTATACGAGGAAATCTTATATCTGGAGCACCAATGAGAAGTGGAACTAT TCAATTTCCAAACCCTCCAATTATTATTGGTATAACTATGAAAAAAATTA TAACAAAAGCATGAGCAGTAACAATTACATTATAAAAATGCTCGTCAATT AAAACTATAGATGTACCTAATTCTAAACGAATTAATAANNACAAACCTGT TCCAACTAAACCACATCATACACCAAAAACTATATATAAAGTACCNATAT CTTTATGATTTGNNGACNNN >20-11_16F NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNANATNNNNNNNNNNN NNNNNNNCANTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNN >21-11_CF NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNTNNNNNNNANNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNGNGNNNNNNNGNGNGNNNNNNNNNNTNNNNN NNNNNNNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >22-12_16R NNNNNNNNNNNNNNNNATCTTTAGNNNTGTNAGTGNNNNNGTTCNNNNNN NNCATCGAGGTCACAAACNNNNNNNNNNNNNNNNNGNNNNNNNNAAGGTA GTTTATTATCCNNNNNNNNNNNNNNACATAAAATTAATTAAGTAGAAAAG TTAAACTTGTTTTCTTGTCGCCCCAACAAACAAATAGCTGTTTTAATATT ATATAATAACAGATATATTTAATAACTCTAAGGGTCTTCTCGTCTTTTTT CTTATCACTGGCATTTTCACCAGATAAGTAAATTCAACTAAAACTAAATG TTATAGGTAGTATTCATTTATCCTTTCATACTAGACTACAATTAATAGCC AATTGATTATGCTACCTTAGCACAGTCAAGGTACTGCGGCCGTTAATTAA AAAACACCGGGCAGAAAATACCGATAATATTTAGGCTCTATCGGCTNTNN NTTTNNNNNNNNNNNNNGNNN >23-12_CR NNNNNNNNNNNNNNNNGNNNNNNCCNCCNNNCCTNGNGNNCAAAGAACNN NNNTTAAAGTTTCGATCGGNNNNNNNNNNNNNNNNNNNNNGNNNNNNCAG GAAGAGAGAGAAGNANNNNNNNGNNNNCACTAAGACTGATCACACAAATA AATTTAAGCGCTCGAGAGTTACTCCTGGAGCACGTATGTTTATAATANNT GTAATAAAGTTAATTGCCCCTATAATTGAAGACAGGCCGGCTAAATGAAG AGAAAAGATAGCAAGGTCCACCGAAATACCAGAATGAAATGTTGAACTTG ATAGGGGAGGATATACAGTTCAACCCGTTCCTACTCCCCCTTCAATTATC GAGCTACAGAGTAGTAATACGAAAGAAGGCGGAAGAAGCCAAAAGCTTAT ATTATTTATTCGAGGAAAACTTATATCCGGCGAGCCGATAAGTAAAGGAA CCATTCAATTTCCAAAGCCCCCGATTAAAATAGGTATTACTATGAAAAAA ATCATCACAAAAGCATGAGCTGTCACAATTACATTGTAAAAATGTTCATC CAATAGTACCGTAGATGTTCCAAGCTCTAGCCGAATTAAAATGCTTAACC CTGATCCGACCAAACCACACCAAATTCCAAAAATTAAATATAATGTACCA NTATCTTTATGATTNNNNNNNNNN “*.ABI” Sequenceanalysis?

  5. SEQUENCE BASED IDENTIFICATION 16S COI P1E: Physella acuta 3/4 3/4 L1S: Physella/ 2/4 (4/4) 2/4 (4/4)Pseudosuccinea P2E: Physa sp./ 4/4 1/4Physa gyrina Group 12: PCR 12_2 (CR) to Coen How about BLASTX

  6. >08-4_CR NNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTCCNGCAGGANNNNNNNNNN NNNNTTAAAATTTCGATCTGNNNNNNNNNNNNNNNNNCCNGNNNNNNNTG GTAAAGATAAAAGAANNNNNNNNNNNNNNTAATACAGATCATACAAATAA TCTTATTCGTTCTAATGTAATACCTGGAGATCGTATATTANANNNNNNNN NNNAATAAAATTAATTGCTCCTAAAATCCTGGATAAACCGGCTAAATGTA AAGAAAAAATAGCTAAATCAACAGAAGATCCACCATGAGCAATAGGTCCA CTCAATGGTGGGTAAACTGTTCATCCAGTACCTACCCCACCTTCTACTAT TCTAGAGCAAAGTAAGAGAATAAACGAAGGTGGTAGTAATCAAAATCTTA TATTATTTATACNANGAAATCTTATATCTGGNGCANCAATGANAAGTGNA ACTATTCANTTTCNAAACCNNNCANTNATNNTTGGTATAACNATGAAAAA AATNNTAACNAANNNNNNGAGCNGNANNNNNNNCNTTNNNNAAAANGNTC GNCAATNNAANNNNNNNNNNNNNNCNNNNTNNAANNAANNNNNNNNNNNA NNCNNNNNNNNNNANCNNNNNNNNNNNNCNAAANNNNNNNNNANGNNCNN NNNNNTNNNNNATTNNNNNNNNN L1S COI: Encodes a protein So?

  7. >08-4_CR NNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTCCNGCAGGANNNNNNNNNN NNNNTTAAAATTTCGATCTGNNNNNNNNNNNNNNNNNCCNGNNNNNNNTG GTAAAGATAAAAGAANNNNNNNNNNNNNNTAATACAGATCATACAAATAA TCTTATTCGTTCTAATGTAATACCTGGAGATCGTATATTANANNNNNNNN NNNAATAAAATTAATTGCTCCTAAAATCCTGGATAAACCGGCTAAATGTA AAGAAAAAATAGCTAAATCAACAGAAGATCCACCATGAGCAATAGGTCCA CTCAATGGTGGGTAAACTGTTCATCCAGTACCTACCCCACCTTCTACTAT TCTAGAGCAAAGTAAGAGAATAAACGAAGGTGGTAGTAATCAAAATCTTA TATTATTTATACNANGAAATCTTATATCTGGNGCANCAATGANAAGTGNA ACTATTCANTTTCNAAACCNNNCANTNATNNTTGGTATAACNATGAAAAA AATNNTAACNAANNNNNNGAGCNGNANNNNNNNCNTTNNNNAAAANGNTC GNCAATNNAANNNNNNNNNNNNNNCNNNNTNNAANNAANNNNNNNNNNNA NNCNNNNNNNNNNANCNNNNNNNNNNNNCNAAANNNNNNNNNANGNNCNN NNNNNTNNNNNATTNNNNNNNNN L1S COI: Encodes a protein So translate and compare Genetic Code? Codons/Reading Frame?

  8. sequencing + strand sense coding primerR A 5’ primerF 3’ A - strand antisense non-coding primerR 3’ primerF 5’ sense GGAA A 5’ ATCG 3’ NEED TO KNOW WHY SEQUENCE THIS? A antisense CCTT 3’ TACG 5’

  9. sequencing forward + strand sense coding primerR A 5’ primerF 3’ A - strand antisense non-coding primerR 3’ primerF 5’ sense GGAA A 5’ ATCG 3’ Forward primer sequencing reaction ATCG 5’ 3’ A - strand antisense non-coding CCTT 3’ TACG 5’

  10. sequencing results + strand sense coding primerR A 5’ primerF 3’ A - strand antisense non-coding primerR 3’ primerF 5’ Forward primer sequencing reaction generates sense strand ATCG ggaa 5’ 3’ A - strand antisense non-coding CCTT 3’ TACG 5’

  11. sequencing reverse + strand sense coding primerR A 5’ primerF 3’ A - strand antisense non-coding primerR 3’ primerF 5’ sense GGAA A 5’ ATCG 3’ A antisense CCTT 3’ TACG 5’

  12. sequencing reverse + STRAND SENSE CODING GGAA A 5’ ATCG 3’ A - strand antisense non-coding cctt 3’ tagc 5’ Reverse primer sequencing reaction SENSE GGAA A 5’ ATCG 3’ CCTT 5’ 3’ A antisense CCTT 3’ TACG 5’

  13. sequencing results + STRAND SENSE CODING GGAA A 5’ ATCG 3’ A - strand antisense non-coding cctt 3’ tagc 5’ Reverse primer sequencing reaction SENSE GGAA A 5’ ATCG 3’ CCTT tagc 5’ generates - strand 3’

  14. sequencing results + STRAND SENSE CODING GGAA A 5’ ATCG 3’ A - strand antisense non-coding cctt 3’ tagc 5’ Reverse primer sequencing reaction SENSE GGAA A 5’ ATCG 3’ CCTT tagc 5’ generates - strand 3’ ABI File generated 5’-3’ Sequence is reverse complement of coding sequence !

  15. Forward primer sequencing reaction sequencing generates + strand ATCG ggaa 5’ 3’ Reverse primer sequencing reaction CCTT tagc 5’ generates - strand 3’ sequencing generates + strand ATCG ggaa 5’ 3’ reverse complement yields + (coding) sequence two confirmatory sets of sequence data

  16. sequencing results + STRAND SENSE CODING GGAA A 5’ ATCG 3’ A - strand antisense non-coding cctt 3’ tagc 5’ Reverse primer sequencing reaction SENSE GGAA A 5’ ATCG 3’ CCTT tagc 5’ generates - strand 3’ ABI File generated 5’-3’ TTCC cgat 3’ 5’ dnarts - setareneg Sequence is reverse complement of coding sequence !

  17. Forward primer sequencing reaction sequencing generates + strand ATCG ggaa 5’ 3’ dye blobs Reverse primer sequencing reaction CCTT tagc 5’ generates - strand 3’ dye blobs

  18. Sequence editing Full length of amplicon? Look for other primer Do we have all information? Edit, compare replicate reactions Compare computationally to other sequences BLAST AND Phylogenetic analysis for “best” identification

  19. So full length? Abrupt end Primer? PRIMERS ARE NOT REAL SEQUENCE BAD ARTEFACTS!!

  20. ? LCO1490: 5'-GGT CAA CAA ATC ATA AAG ATA TTG G -3’ HC02198: 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3’ Primer is reverse complement at end of sequence run

  21. Sequence reverse complemented LCO1490: 5'-GGT CAA CAA ATC ATA AAG ATA TTG G -3’ HC02198: 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3’ Primer is reverse complement at end of seqeunce run

  22. Sequence reverse complemented LCO1490: 5'-GGT CAA CAA ATC ATA AAG ATA TTG G -3’ HC02198: 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3’ Primer is reverse complement at end of sequence run

  23. Fix “N” calls: what are these? Stay at regular spacing distance

  24. Fix “N” calls: what are these? Stay at regular spacing distance

  25. Dye Blobs? Edit under the blob

  26. A G C G T N A A NNNN Dye Blobs? Edit under the blob

  27. A G C G T N A A NNNN T T G A C G A G C A T T T T T A Dye Blobs? Edit under the blob

  28. NextSeq Illumina run, 130 million, 2 x 150 (300nt) Paired End Reads Result: ≤ 3,900,000,000 nucleotides(inspect all nts @1/sec: 365/24/60/60 = ~123 years) Sequence quality: Trimming bad sequence + Filtering to remove adaptors, barcodes Assembly https://www.youtube.com/watch?annotation_id=annotation_1533942809&feature=iv&src_vid=HMyCqWhwB8E&v=fCd6B5HRaZ8

  29. Bring your LAPTOP Use W7 LAPTOP URL: http://emil.unm.edu/galaxy Login: UNM account id without @unm. pw:4546L2018 September 24th, Dr LiJing Bu

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