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Van Dexter exercise 11 #15

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Van Dexter exercise 11 #15

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12e3278
spore fastas combined
svandexter Nov 27, 2018
2379804
problem 1
svandexter Nov 28, 2018
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10 changes: 10 additions & 0 deletions align.sh
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#usage: bash align.sh
#aligns sequences for bioinformatics purposes

for x in *.fasta
do sed -e '$s/$/\n/' -s sporecoat*.fasta > combinedspores.fasta; sed -e '$s/$/\n/' -s transporter*.fasta > combinedtransporter.fasta
done

/afs/nd.edu/user9/svandext/local/bin/muscle3.8.31_i86linux64 -in combinedspores.fasta -out sporesaligned.afa
/afs/nd.edu/user9/svandext/local/bin/muscle3.8.31_i86linux64 -in combinedtransporter.fasta -out transporteraligned.afa

52 changes: 52 additions & 0 deletions gene_sequences/combined.fasta
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>Q8XVY0_RALSO/26164
TTTTFSVSTTVNATCVINSASALTFAAFDPSQGAQASTSSISVNCTNTTPFNIGLNAGTGTGATVASRVMTSGANTLTYSLYQDSGHASVWGNTVGTNTVAGTGAGMAAGNAITKTVYGLIPSQPNTVPGNYADTVTVT
>Q0BSH7_GRABC/37169
TTTTFQVTATVQASCIIQATNLSFGNYSGSQTDATSTIQVTCTNSTPYNVGLSAGTGSGATVSNRKMSLNSTSALPYALYSDASRSTNWGNTPNQDTVSGTGNGSAQSLTVYGRIQTGNYPTPGSYADTITAT
>Q0AAK3_ALKEH/24160
DTATFDVTATVDPTCTVDADNLVFGTYDPFSDTPLDENSEIRVQCTSDTPYDIGLDDGDNTGAEGERRMALADESDFLEYDLYHDNHGGTSWGDIDSGAELTGLSGTGSEQSYVVYGRIFAEQSVAVGNYVDTIEVT
>Q8XPY6_RALSO/36170
KTTTFTVSLTLQADCSISANALNFGTQGVLAANVDQTATLSVTCSNTAPYNVGFDAGTTTGSTIAARLLAGSGAATVGFQLYSDSARTQIWGNTVGTDTVSGTGSGTAQVLTVYGRVPSQNSPAAGTYSTTITAT
>Q63W79_BURPS/31169
ATATFTVSLTIQANCTISANALSFGTNGVLATAVNQQTTLSVTCSNTTSYNVGLDAGNVSGSTVSSRLLAGTTTGNTSTTVSFQLYQDSGHTTIWGNTVGTNTVSGTGNGTAQTLSVYGQVPAQTTPKPDTYESTVTAT
>Q7CVQ4_AGRFC/27162
ATTNFNVQITIQAACQINSAGNLDFGTNGVIGAPIDVTSQIVVQCTASTPFSLGLSAGAGSGATVANRLMTSAAGATISYSLYTTAAHSTVWGNTVGTDRQTGTGTGAPQNFTVFGRVPAQTTPAVGVYTDTVTAT
>Q985D5_RHILO/27162
ATGNMTVRITIQAECKVQTATDMDFGTNGVIDANVDQTSTISVQCTNSTPYNVGLSAGVGAGATVAVRKMTGPAAAVLNYSLYRDVARAQLWGTTIGTDTVAGTGNGAAQPLTVYGRVPPQTTPGAGVYTDTVAIT
>A6X8A6_OCHA4/27162
ATGNMNVRITIQAECKIVTATDLDFGTKGVIDVNVDQTSTISVQCTNGTPYTVGLSAGGGAGATVAMRKMTGAASATINYTIYRDAARTQVWGVTAGTDVVSGTGNGNAQSITAYGRVPAQTTPAPGVYSDVVSVT
>A9CH19_AGRFC/182313
TQVPFTVSAAVAPTCIISAQNINFGSHGVLNTAVDANGAINLTCTNGLNYSVALNGGLSNSPPAARQMVQGAASIIYGLYRDVSRTNVWGSAAGQIATGTGNGSLQTLTVFGRVPAQNTPAPGNYADTVVVT
>Q985D8_RHILO/205338
DRPTFTINAIVPANCLLAIQNIDFGSNGILGANVDATGGVSITCTPGTPYTVSLSNGTTGSAPTARKMSKGVETVTYGLYKDNARSQVWGDAAMPGSTVAGSGSGAAQNLTIYGRVPAQTTPSAGVYTDTVVVT
>A7H7Q6_ANADF/25150
ATAQFQVTATVVKKCKISATTIAFGNYDPATILSAEGTLTLKCTKGTLYSVALDGGSTGSRQMTQAAEVLDYELYSDAGHTAVWPSTAAAPSVAAAGADEALIIFAQVPADQYPAPGAYADTVTAT
>Q2IFL0_ANADE/27162
ATATLDVTATVVPSCTIAATPVAFGSYDPLVTNAATALDAQGTVTVTCTTGTAYTVGLGAGNSGSGSRAMQHASIAGAQLPYELYQEAARTTVWDSTVMQAGTAASITPVQYTVYGRIPAAQNVPTGNYADAVVAT
>Q0C623_HYPNA/23151
ANGTLDVQATVVNTCVVLTAPVVFASVGLDEVTANGSITVNCTNTSAFTVALDGGDSGDISARSLTHASLPASFNYQLYTDAGLTTVWGDGVTGSQANGSGPSQTLTVYGRTTSTPDTAGAYADEVQVT
>Q63W78_BURPS/193326
TFAFTASATVVNDCFINATNVAFGSTGVIQGALTATGTISAQCTNGDAFRIALNGGASGNVAARAMQRTGGGGAVNYQLYLDAAHSTIWGDGTAGTSTATGTGSGLSQSLTVYGQVPAQTTPAPGTYSDTITAT
>Q8XVY3_RALSO/23163
VLVALASWAPGALAVSCSVSANALSFGAYNTTSNLTGTTTVTITCGAWGGASSINYTLSASVGSGTYANRQVLNGSNVIAYNLYTTSADTSIWGDGNGDGTVTLSGTVTKQVGTVNLTIYGKINGGQNVVPGSYATTIPIT
>Q8XPY9_RALSO/25163
ASAQSCSVASASLNFGSISPVQAGNTDTSTTLTVSCSGFLLQGTVARACLNLGVGSGDTGISPRVLSAGANQLQYNLYADSARSVVWGGRTTPATPAIQVDVSLGLLGFGSATVTVYGRVPGGQTTVPAGAYTQSFSGT
>A9CH19_AGRFC/11158
IAAAFVASPVLAQSCTFSMSDMNFGFVNLAGGAAVDTTATLSVTCNNPLSLALSIRICPNINAGGGGQSGGIRRMLQGSNILNYQLYQTSARTTAWGSVTQPALGAPPPIDMALPLLINSTTRTVYGRINAGQASAARGLYLSSFAGG
>Q985D8_RHILO/37183
SAALLLPTVAWAQSCSFGVSAMNFGLVDTLSGSSSNSTATLSVNCTGLLLQRILVCPNLGTGSGGATASARQMLSGANDLNYQLYSDSARSVVWGSYAWPYPPTAPGFALTLNVLGSGSASQTIYGAILGGQATAVPSTYLSTFSGS
>Q3A2W0_PELCD/10150
IIVLLFAVDAYAFHCEVTTTPVSFGAYDVFSSFSLDTTGRISVSCNNPEKKRMPVTISISRGAANSFSPRQMRRIGGSDRMDYYLFVDASRTAVWGDGTGGSSTYVGMIDRTSPLNVPIYGRIPARQNLRAGSYQDILVVT
>A7H7Q5_ANADF/16150
APRAVDAAQPPSPGPSCSVSAGSVAFGAYDPLSPTHLDSTGTIGLTCAVRQLVTISLGTGQSGTFARELRGPGGAALRYDLYTDATRTQVWGDGTAGTATWPFETERGRYVPVYARVLAGQDVPAGPYSDTIVVT
>Q2IFK8_ANADE/19157
ATALSLVAPAAARAASCSLTMGTSIAFGAYDPLSPVPLTTTGMLQYRCSRGQPIRITFTAGSSGDVYARTLRQGPWTLAYNLYADAGFGTVWGDGTGGTAAAPAVTTLSNGLTVAYVFGRIPARQEPPVGPYSDTIVVT
>Q1D5L1_MYXXD/13153
AVAGVCGLLPGLAGAVCQIRSTIGVSFGTYLTTDLLPRDSAGSITYRCEGQITPITIDFSAGGSGTPLARSMAGPGAQRLEYNLYVDATRLIVWGNGTSGTGRYGPVVPLFGVEVTVPIFGRIPAGQAIPAGAYADTVVMT
>Q60C08_METCA/20167
LLACPKISDADPYQCDIGNISVPHAVYDPTDSNPNSSGVGTVGITCHLKNAKQTQQVQYTIALSRGSSGSYNPRRMSGGRGSLGYNLYLDAARVTIWGDGSGGTFPLRGTLLLNPTTPVQQVIHNIYGLIPPLQDVYAGTYTDTVTIT
>Q0AAK6_ALKEH/8153
SLFLVAAGSGSAQAYTCSISADPLAFGQYDPITGAQVDGASEVSVSCSLLGLVSLLVSYEISLDPGTGGSYHPRALSSATDTLDYNLYVDTARTEIWGDGTDDTATVTDSYTLGVLTVTRYYPVYGRVFADQNVAAGVYDDTITAT
>Q12FX3_POLSJ/50194
TWGVLLAAGTAHATISCSVSGNGFTSVYDPISTVPNDNVSSVTINCSRASGDPTTTTYSLASTNGLYPQGQNNRAYYPTNKYLKYDIYKDAAYSSRWGPGGSAPFTGTLNFGSGTSASLTLPYYNRVAAQQSAVAADYTDTMTAT
>A1VIJ0_POLNA/19170
ALFLLLATAGPAQAGSCTVGSSGLAFGAYQPLTFAGKLTSSAVTSNASISVVCTGIASGGAYSIALGPSTTGSGDRISTRYLGNSNGGDDMSFNIYTSASYSTVWGNGTTGGLVGGSIPVGDSNQSQPVYGRIAASQNTLRAGSYSGSLTMT
8 changes: 8 additions & 0 deletions gene_sequences/combined2.fasta
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>LACY_CITFR/1412
MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQPIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNAGAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVILALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIMSVRIIGSHSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE
>LACY_KLEOX/6416
LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQPVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSSRSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALILGVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFDQQFANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIMSVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQLSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTLKGSKTLLPATA
>RAFB_ECOLX/4415
ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQPLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSAGAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLLLLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFDQQFAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIMTIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQLAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLSSSPGIVHPSVE
>A0A026RKY7_ECOLX/4411
NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRFKDKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV