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Susi Submission #17

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Susi Submission #17

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5c43a96
Combining fasta files
aliciasusi Nov 27, 2018
e61902e
Combining fasta files part 2
aliciasusi Nov 27, 2018
a96d5c7
Shell script for Problem 1
aliciasusi Nov 28, 2018
eef8883
Shell Script for Problem 2
aliciasusi Nov 28, 2018
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12 changes: 12 additions & 0 deletions HMMtransporter.sh
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#!/bin/bash
/afs/nd.edu/user17/asusi/local/bin/hmmbuild transporterAll.hmm transporterAll.fasta.align
for file in proteomes/*.fasta
do
/afs/nd.edu/user17/asusi/local/bin/hmmsearch --tblout $file.tbl transporterAll.hmm $file
done
for file in proteomes/*.tbl
do
echo "$file" >> matches.all
cat $file | grep -v "#" | wc -l | cut -d ' ' -f 1 >> matches.all
done

15 changes: 15 additions & 0 deletions gene_sequences/SporeGene.sh
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#!/bin/bash
for file in sporecoat0*.fasta
do
sed -e '$s/$/\n/' $file
done > sporecoatAll.fasta
for file in transporter0*.fasta
do
sed -e '$s/$/\n/' $file
done > transporterAll.fasta

for file in *All.fasta
do
/afs/nd.edu/user17/asusi/local/bin/muscle -in $file -out /afs/nd.edu/user17/asusi/local/bin/IBC_EX11/$file.align
done

5 changes: 5 additions & 0 deletions gene_sequences/TransporterGene.sh
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#!/bin/bash
for file in transporter0*.fasta
do
sed -e '$s/$/\n/' $file
done > transporterAll.fasta
52 changes: 52 additions & 0 deletions gene_sequences/sporecoatAll.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/transporterAll.fasta
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>LACY_CITFR/1412
MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQPIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNAGAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVILALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIMSVRIIGSHSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE
>LACY_KLEOX/6416
LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQPVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSSRSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALILGVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFDQQFANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIMSVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQLSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTLKGSKTLLPATA
>RAFB_ECOLX/4415
ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQPLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSAGAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLLLLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFDQQFAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIMTIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQLAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLSSSPGIVHPSVE
>A0A026RKY7_ECOLX/4411
NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRFKDKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV