From 89096ad1f1fcece19cd57734c2566be6b988f7d7 Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 13:59:59 +0300 Subject: [PATCH 01/10] coronavirus.fasta.CAST_thr20_4hackathon.tab Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. Regions are colored according to amino acid type, following the Rasmol color scheme as described in http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. --- ...oronavirus.fasta.CAST_thr20_4hackathon.tab | 99 +++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab diff --git a/DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab b/DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab new file mode 100644 index 0000000..010f0e4 --- /dev/null +++ b/DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab @@ -0,0 +1,99 @@ +P0DTD1 928 1015 #E60A0A E-rich region (80) +P0DTD1 3583 3695 #E6E600 M-rich region (41) +P0DTD1 1192 1247 #E60A0A E-rich region (39) +P0DTD1 5328 5354 #E6E600 C-rich region (38) +P0DTD1 3978 4024 #145AFF K-rich region (36) +P0DTD1 2327 2359 #3232AA F-rich region (34) +P0DTD1 2149 2206 #FA9600 T-rich region (32) +P0DTD1 4326 4332 #E6E600 C-rich region (30) +P0DTD1 2384 2399 #3232AA Y-rich region (30) +P0DTD1 3583 3595 #0F820F L-rich region (28) +P0DTD1 3939 3969 #C8C8C8 A-rich region (26) +P0DTD1 6132 6135 #E6E600 C-rich region (26) +P0DTD1 4244 4279 #C8C8C8 A-rich region (25) +P0DTD1 1473 1522 #FA9600 S-rich region (25) +P0DTD1 1426 1447 #FA9600 T-rich region (24) +P0DTD1 3204 3217 #3232AA Y-rich region (24) +P0DTD1 981 998 #E60A0A D-rich region (23) +P0DTD1 126 138 #EBEBEB G-rich region (23) +P0DTD1 3098 3115 #3232AA Y-rich region (23) +P0DTD1 3152 3160 #3232AA Y-rich region (23) +P0DTD1 4845 4850 #3232AA Y-rich region (23) +P0DTD1 2750 2796 #0F820F V-rich region (23) +P0DTD1 4449 4456 #E60A0A D-rich region (22) +P0DTD1 2226 2254 #0F820F L-rich region (22) +P0DTD1 2364 2387 #E6E600 M-rich region (22) +P0DTD1 6987 6988 #B45AB4 W-rich region (22) +P0DTD1 4041 4051 #00DCDC N-rich region (21) +P0DTD1 1068 1074 #EBEBEB G-rich region (21) +P0DTD1 1194 1233 #145AFF K-rich region (21) +P0DTD1 3602 3614 #3232AA F-rich region (21) +P0DTD1 6065 6067 #DC9682 P-rich region (21) +P0DTD1 2544 2558 #FA9600 S-rich region (21) +P0DTD1 4158 4175 #FA9600 T-rich region (21) +P0DTD1 3783 3804 #3232AA F-rich region (20) +P0DTD1 3453 3467 #FA9600 T-rich region (20) +P0DTD1 1418 1425 #3232AA Y-rich region (20) +P0DTD1 4678 4687 #3232AA Y-rich region (20) +P0DTD1 6369 6372 #3232AA Y-rich region (20) +P0DTC1 928 1015 #E60A0A E-rich region (80) +P0DTC1 3583 3695 #E6E600 M-rich region (41) +P0DTC1 1192 1247 #E60A0A E-rich region (39) +P0DTC1 3978 4024 #145AFF K-rich region (36) +P0DTC1 2327 2359 #3232AA F-rich region (34) +P0DTC1 2149 2206 #FA9600 T-rich region (32) +P0DTC1 4326 4332 #E6E600 C-rich region (30) +P0DTC1 2384 2399 #3232AA Y-rich region (30) +P0DTC1 3583 3595 #0F820F L-rich region (28) +P0DTC1 3939 3969 #C8C8C8 A-rich region (26) +P0DTC1 4244 4279 #C8C8C8 A-rich region (25) +P0DTC1 1473 1522 #FA9600 S-rich region (25) +P0DTC1 1426 1447 #FA9600 T-rich region (24) +P0DTC1 3204 3217 #3232AA Y-rich region (24) +P0DTC1 981 998 #E60A0A D-rich region (23) +P0DTC1 126 138 #EBEBEB G-rich region (23) +P0DTC1 3098 3115 #3232AA Y-rich region (23) +P0DTC1 3152 3160 #3232AA Y-rich region (23) +P0DTC1 2750 2796 #0F820F V-rich region (23) +P0DTC1 2226 2254 #0F820F L-rich region (22) +P0DTC1 2364 2387 #E6E600 M-rich region (22) +P0DTC1 4041 4051 #00DCDC N-rich region (21) +P0DTC1 1068 1074 #EBEBEB G-rich region (21) +P0DTC1 1194 1233 #145AFF K-rich region (21) +P0DTC1 3602 3614 #3232AA F-rich region (21) +P0DTC1 2544 2558 #FA9600 S-rich region (21) +P0DTC1 4158 4175 #FA9600 T-rich region (21) +P0DTC1 3783 3804 #3232AA F-rich region (20) +P0DTC1 3453 3467 #FA9600 T-rich region (20) +P0DTC1 1418 1425 #3232AA Y-rich region (20) +P0DTC2 1235 1254 #E6E600 C-rich region (74) +P0DTC2 672 751 #FA9600 S-rich region (30) +P0DTC2 1212 1217 #B45AB4 W-rich region (28) +P0DTC2 437 450 #00DCDC N-rich region (25) +P0DTC2 924 975 #FA9600 S-rich region (23) +P0DTC2 1257 1262 #E60A0A D-rich region (22) +P0DTC2 1224 1234 #0F820F I-rich region (22) +P0DTC2 716 739 #FA9600 T-rich region (21) +P0DTC3 83 129 #0F820F L-rich region (32) +P0DTC3 204 215 #3232AA Y-rich region (22) +P0DTC3 268 273 #FA9600 T-rich region (21) +P0DTC3 105 114 #3232AA Y-rich region (21) +P0DTC4 12 39 #0F820F L-rich region (37) +P0DTC4 40 44 #E6E600 C-rich region (25) +P0DTC5 22 67 #0F820F L-rich region (25) +P0DTC5 202 216 #00DCDC N-rich region (20) +P0DTC6 9 37 #0F820F I-rich region (24) +P0DTC7 100 116 #0F820F I-rich region (23) +P0DTC7 1 12 #0F820F L-rich region (20) +P0DTD8 1 34 #0F820F L-rich region (40) +P0DTD8 9 30 #3232AA F-rich region (21) +P0DTC9 173 267 #FA9600 S-rich region (63) +P0DTC9 367 390 #145AFF K-rich region (40) +P0DTC9 228 306 #00DCDC Q-rich region (31) +P0DTC9 2 49 #00DCDC N-rich region (27) +P0DTC9 108 112 #3232AA Y-rich region (26) +P0DTC9 248 266 #145AFF K-rich region (25) +P0DTC9 377 418 #00DCDC Q-rich region (22) +P0DTC9 88 95 #145AFF R-rich region (20) +P0DTD3 52 71 #0F820F L-rich region (35) +P0DTD3 68 70 #E6E600 C-rich region (27) From 436724c70b6e4c412e6a35178b1e157b1f09b553 Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:03:59 +0300 Subject: [PATCH 02/10] Create README --- DARK/README | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 DARK/README diff --git a/DARK/README b/DARK/README new file mode 100644 index 0000000..8771aad --- /dev/null +++ b/DARK/README @@ -0,0 +1,7 @@ +Contents of covid-19-Annotations-on-Structures/DARK + +- coronavirus.fasta.CAST_thr20_4hackathon.tab +Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). +CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. +Regions are colored according to amino acid type, following the Rasmol color scheme as described in +http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. From 4ce483e75463cfb22c59ae1c4f375f3b6e9ff16c Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:05:17 +0300 Subject: [PATCH 03/10] Add files via upload --- DARK/casttab2swmodel.pl | 65 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 DARK/casttab2swmodel.pl diff --git a/DARK/casttab2swmodel.pl b/DARK/casttab2swmodel.pl new file mode 100644 index 0000000..ef544e4 --- /dev/null +++ b/DARK/casttab2swmodel.pl @@ -0,0 +1,65 @@ +#!/usr/bin/perl +use strict; +use warnings; + +# Description +# ----------- +# Code to reformat CAST output for the covid-19-Annotations-on-Structures +# project https://github.com/gtauriello/covid-19-Annotations-on-Structures + +# +# Author: Vasilis J Promponas +# Contact: vprobon@ucy.ac.cy; vasilis.promponas@gmail.com +# + +my %colorscheme = getColorScheme(); + +my @annot = (); +open(CASTTAB, $ARGV[0]) or die "Could not open CAST tab ($ARGV[0])"; +my $entry = ; # Read header line + +while($entry = ) +{ +# Input format (tab separated): +# >sp|P0DTD3|Y14_WCPV Uncharacterized protein 14 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF14 PE=3 SV=1 C 68 70 27 + chomp($entry); + next if $entry eq ''; + my @tmp = split(/\t/,$entry); + my $aatype = $tmp[1]. '-rich region (' . $tmp[4]. ')'; + my $from = $tmp[2]; + my $to = $tmp[3]; + my @tmp2 = split(/\|/, $tmp[0]); + my $uniprot_id = $tmp2[1]; + my $color = $colorscheme{$tmp[1]}; + my $out = join("\t", ($uniprot_id, $from, $to, $color, $aatype,)) . "\n"; + push @annot, $out; +} +close(CASTTAB); + + +foreach my $annotation (@annot) +{ + print $annotation; +} + + +sub getColorScheme +{ + # Return a hash mapping the Rasmol color scheme + # See http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM + my %colors=(); + $colors{'D'} = $colors{'E'} = '#E60A0A'; + $colors{'C'} = $colors{'M'} = '#E6E600'; + $colors{'K'} = $colors{'R'} = '#145AFF'; + $colors{'S'} = $colors{'T'} = '#FA9600'; + $colors{'F'} = $colors{'Y'} = '#3232AA'; + $colors{'N'} = $colors{'Q'} = '#00DCDC'; + $colors{'G'} = '#EBEBEB'; + $colors{'L'} = $colors{'V'} = $colors{'I'} = '#0F820F'; + $colors{'A'} = '#C8C8C8'; + $colors{'W'} = '#B45AB4'; + $colors{'H'} = '#8282D2'; + $colors{'P'} = '#DC9682'; + + return(%colors); +} From 5c2b1107fa9be1422be1f66728a8851833a796b3 Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:08:32 +0300 Subject: [PATCH 04/10] Update README --- DARK/README | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/DARK/README b/DARK/README index 8771aad..c4cf64f 100644 --- a/DARK/README +++ b/DARK/README @@ -5,3 +5,7 @@ Compositionally biased regions detected by the CAST algorithm (Promponas et al., CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. Regions are colored according to amino acid type, following the Rasmol color scheme as described in http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. + +- casttab2swmodel.pl +Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. +No external dependencies. From 6a8b887fad03c50f32ae7925e90ae3e5ad727e75 Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:27:55 +0300 Subject: [PATCH 05/10] Add files via upload --- DARK/coronavirus.fasta.CASTV2.2.thr20 | 261 ++++++++++++++++++++++++++ 1 file changed, 261 insertions(+) create mode 100644 DARK/coronavirus.fasta.CASTV2.2.thr20 diff --git a/DARK/coronavirus.fasta.CASTV2.2.thr20 b/DARK/coronavirus.fasta.CASTV2.2.thr20 new file mode 100644 index 0000000..e9c4d4a --- /dev/null +++ b/DARK/coronavirus.fasta.CASTV2.2.thr20 @@ -0,0 +1,261 @@ +>sp|P0DTD1|R1AB_WCPV Replicase polyprotein 1ab OS=Wuhan seafood market pneumonia virus OX=2697049 GN=rep PE=1 SV=1 +MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV +LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK +VLLRKNXNKXAXXHSYXADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG +AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW +YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI +RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL +PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC +AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF +SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA +ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY +ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV +GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC +VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG +TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN +ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEW +SMATYYLFDESGEFKLASHMYCSFYPPDXDXXXGDCXXXXFXPSTQYXYGTXDDYQGKPL +XFGATSAALQPXXXQXXDWLXXXSQQTVGQQXGSXXNQTTTIQTIVXVQPQLXMXLTPVV +QTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHXXXVAXALNKATN +NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQ +HEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLXMXSXXQVX +QXIAXIPXXXVXPFITXSXPSVXQRXQDDXXIXACVXXVTTTLXXTKFLTENLLLYIDIN +GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV +PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLA +HAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDXGARFXFXXSKXXVASLINXLND +LNEXLVXMPLGYVTHGLNLEEAARYMRSLKVPATVXVXXPDAVTAYNGYLTXXXKTPEEH +FIETIXLAGXYKDWXYXGQXTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLL +SLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV +LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL +LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN +LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ +ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK +GPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPY +PNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFK +KGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLA +CEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYV +DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSXXXNIVXRC +LNRVCXNYMPYFFXLLLQLCXFXRSXNSRIKASMPXXIAKNXVKSVGKFCLEASFNYLKS +PNFSKXINIIIWFXXXSVCXGSXIYSTAAXGVXMSNLGMPSYCTGYREGYLNSTNVTIAT +YCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWXLAYILXTRXXYV +LGLAAIMQLXXSYXAVHXISNSWLXWLIINLVQXAPISAXVRXXIFFASFXXVWKSXVHV +VDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCA +GSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH +FVNLDNLRANNTKGSLPINVIVFDGKXKCEEXXAKXAXVYYSQLMCQPILLLDQALVSDV +GDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQG +FVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN +AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQXXNXXTTKIAL +KGGKIXNNWLKQLIKXTLXFLFXAAIFYLITPXHXMSKHTDFSSEIIGYKAIDGGVTRDI +ASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD +FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE +GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVST +SGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL +AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVXSFLPGVXSVIXLXLTFXLTNDV +SFLAHIQWMVMFTPLVPFWITIAYIICISTKHFXWFFSNXLKRRVVFNGVSFSTFEEAAL +CTFLLNKEMYLKLRSDVLLPLTQXNRXLALXNKXKXFSGAMDTTSYREAACCHLAKALND +FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVY +CPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK +TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV +SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQXAQAAGXDXXIXVNVLAWLYAAVINGDR +WFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN +GRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWXXXTIXTSXXVXVQSTQW +SLXXXLYENAXLPXAXGIIAXSAFAXXFVKHKHAFLCLFLLPSLATVAYFNXVYXPASWV +XRIXTWLDXVDTSLSGFKLKDCVXYASAVVLLILXTARTVYDDGARRVWTLMNVLTLVYK +VYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM +LVYCXLGYXCTCYXGLXCLLNRYXRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKL +NIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILL +AKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRXTLQXIXSEFSSLPSYXXFXTX +QEXYEQXVXNGDSEVVLXXLXXSLNVAXSEFDRDAAMQRXLEXMADQAMTQMYXQARSED +XRAXVTSAMQTMLFTMLRKLDXDALXXIIXXARDGCVPLNIIPLTTAAKLMVVIPDYNTY +KNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ +NNELSPVALRQMSCAAGXXQXACXDDNALAYYNXXKGGRFVLALLSDLQDLKWARFPKSD +GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLXXTVRLQXGNXTEV +PXNSTVLSFCXFXVDXXKXYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES +FGGASXXLYXRXHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYG +CSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKF +LKTNCCRFQEKXEXXNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDG +DMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVEN +PDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPG +SGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRXFK +XWDQTXHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF +RELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQ +TVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDXDXXRXNLPTMCDIRQ +LLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALF +AYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVV +IGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL +SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALL +STDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNS +TYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVY +LPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYI +RKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGAXVLXNSQTSLRX +GAXIRRPFLXXKXXYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK +PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAE +TLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIG +EYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTL +NISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDA +LCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEI +SMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM +FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVV +REFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSC +NVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVI +TGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFIT +REEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSR +VSAKXXXGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM +KYFVKIGPERTXXLXDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQS +NHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHM +VVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSD +KFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSA +FVNLKQLPFFXXSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYL +DAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN +NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDY +KRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSV +KGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQ +MEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDF +IPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEIS +FMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM +NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLND +FVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLA +LGGSVAIKITEHSWNADLYKLMGHFAXXTAFVTNVNASSSEAFLIGCNYLGKPREQIDGY +VMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLII +RENNRVVISSDVLVNN +>sp|P0DTC1|R1A_WCPV Replicase polyprotein 1a OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1 +MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV +LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK +VLLRKNXNKXAXXHSYXADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG +AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW +YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI +RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL +PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC +AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF +SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA +ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY +ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV +GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC +VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG +TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN +ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEW +SMATYYLFDESGEFKLASHMYCSFYPPDXDXXXGDCXXXXFXPSTQYXYGTXDDYQGKPL +XFGATSAALQPXXXQXXDWLXXXSQQTVGQQXGSXXNQTTTIQTIVXVQPQLXMXLTPVV +QTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHXXXVAXALNKATN +NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQ +HEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLXMXSXXQVX +QXIAXIPXXXVXPFITXSXPSVXQRXQDDXXIXACVXXVTTTLXXTKFLTENLLLYIDIN +GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV +PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLA +HAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDXGARFXFXXSKXXVASLINXLND +LNEXLVXMPLGYVTHGLNLEEAARYMRSLKVPATVXVXXPDAVTAYNGYLTXXXKTPEEH +FIETIXLAGXYKDWXYXGQXTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLL +SLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV +LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL +LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN +LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ +ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK +GPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPY +PNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFK +KGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLA +CEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYV +DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSXXXNIVXRC +LNRVCXNYMPYFFXLLLQLCXFXRSXNSRIKASMPXXIAKNXVKSVGKFCLEASFNYLKS +PNFSKXINIIIWFXXXSVCXGSXIYSTAAXGVXMSNLGMPSYCTGYREGYLNSTNVTIAT +YCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWXLAYILXTRXXYV +LGLAAIMQLXXSYXAVHXISNSWLXWLIINLVQXAPISAXVRXXIFFASFXXVWKSXVHV +VDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCA +GSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH +FVNLDNLRANNTKGSLPINVIVFDGKXKCEEXXAKXAXVYYSQLMCQPILLLDQALVSDV +GDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQG +FVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN +AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQXXNXXTTKIAL +KGGKIXNNWLKQLIKXTLXFLFXAAIFYLITPXHXMSKHTDFSSEIIGYKAIDGGVTRDI +ASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD +FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE +GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVST +SGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL +AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVXSFLPGVXSVIXLXLTFXLTNDV +SFLAHIQWMVMFTPLVPFWITIAYIICISTKHFXWFFSNXLKRRVVFNGVSFSTFEEAAL +CTFLLNKEMYLKLRSDVLLPLTQXNRXLALXNKXKXFSGAMDTTSYREAACCHLAKALND +FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVY +CPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK +TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV +SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQXAQAAGXDXXIXVNVLAWLYAAVINGDR +WFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN +GRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWXXXTIXTSXXVXVQSTQW +SLXXXLYENAXLPXAXGIIAXSAFAXXFVKHKHAFLCLFLLPSLATVAYFNXVYXPASWV +XRIXTWLDXVDTSLSGFKLKDCVXYASAVVLLILXTARTVYDDGARRVWTLMNVLTLVYK +VYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM +LVYCXLGYXCTCYXGLXCLLNRYXRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKL +NIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILL +AKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRXTLQXIXSEFSSLPSYXXFXTX +QEXYEQXVXNGDSEVVLXXLXXSLNVAXSEFDRDAAMQRXLEXMADQAMTQMYXQARSED +XRAXVTSAMQTMLFTMLRKLDXDALXXIIXXARDGCVPLNIIPLTTAAKLMVVIPDYNTY +KNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ +NNELSPVALRQMSCAAGXXQXACXDDNALAYYNXXKGGRFVLALLSDLQDLKWARFPKSD +GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLXXTVRLQXGNXTEV +PXNSTVLSFCXFXVDXXKXYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES +FGGASXXLYXRXHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYG +CSCDQLREPMLQSADAQSFLNGFAV +>sp|P0DTC2|SPIKE_WCPV Spike glycoprotein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=S PE=3 SV=1 +MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS +NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV +NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE +GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT +LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK +CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN +CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD +YNYKLPDDFTGCVIAWXSXXLDSKVGGXYXYLYRLFRKSNLKPFERDISTEIYQAGSTPC +NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN +FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP +GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY +ECDIPIGAGICAXYQTQTNXPRRARXVAXQXIIAYTMXLGAENXVAYXNNXIAIPXNFXI +XVXXEILPVXMXKXXVDCXMYICGDXTECXNLLLQYGSFCTQLNRALTGIAVEQDKNTQE +VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC +LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM +QMAYRFNGIGVTQNVLYENQKLIANQFNXAIGKIQDXLXXTAXALGKLQDVVNQNAQALN +TLVKQLXXNFGAIXXVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA +SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA +ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP +LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL +QELGKYEQYIKXPXYIXLGFIAGLXAXVMVTXMLXXMTSXXSXLKGXXSXGSXXKFXEXX +SEPVLKGVKLHYT +>sp|P0DTC3|AP3A_WCPV Protein 3a OS=Wuhan seafood market pneumonia virus OX=2697049 GN=3a PE=3 SV=1 +MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS +KIITLKKRWQLALSKGVHFVCNXXXXFVTVYSHXXXVAAGXEAPFXXXXAXVXFXQSINF +VRIIMRXWXCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS +EHDYQIGGYTEKWESGVKDCVVLHSXFTSDXXQLXSTQLSTDTGVEHVTFFIYNKIVDEP +EEHVQIHTIDGSSGVVNPVMEPIYDEPXXXXSVPL +>sp|P0DTC4|VEMP_WCPV Envelope small membrane protein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=E PE=3 SV=1 +MYSFVSEETGTXIVNSVXXFXAFVVFXXVTXAIXTAXRXXAYXXNIVNVSLVKPSFYVYS +RVKNLNSSRVPDLLV +>sp|P0DTC5|VME1_WCPV Membrane protein OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1 +MADSNGTITVEELKKLLEQWNXVIGFXFXTWICXXQFAYANRNRFXYIIKXIFXWXXWPV +TXACFVXAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL +NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK +LGASQRVAGDSGFAAYSRYRIGXYKLXTDHSSSSDXIALLVQ +>sp|P0DTC6|NS6_WCPV Non-structural protein 6 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=6 PE=3 SV=1 +MFHLVDFQVTXAEXLLXXMRTFKVSXWNLDYXXNLXXKNLSKSLTENKYSQLDEEQPMEI +D +>sp|P0DTC7|NS7A_WCPV Protein 7a OS=Wuhan seafood market pneumonia virus OX=2697049 GN=7a PE=3 SV=1 +MKIIXFXAXITXATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFS +TQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPXFLXVAAXVFXTLCFTLKRKT +E +>sp|P0DTD8|NS7B_WCPV Protein non-structural 7b OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1 +MIEXSXIDXYXCXXAXXXXXVXIMXIIXWXSXEXQDHNETCHA +>sp|P0DTC8|NS8_WCPV Non-structural protein 8 OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1 +MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL +CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF +I +>sp|P0DTC9|NCAP_WCPV Nucleoprotein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=N PE=3 SV=1 +MSDXGPQXQRXAPRITFGGPSDSTGSXQXGERSGARSKQRRPQGLPXXTASWFTALTQHG +KEDLKFPRGQGVPINTNSSPDDQIGYYXXATXXIXGGDGKMKDLSPRWXFXXLGTGPEAG +LPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGXRGGX +QAXXRXXXRXRNXXRNXTPGXXRGTXPARMAGNGGDAALALLLLDRLNXLEXKMXGKGXX +XXGXTVTXXXAAEAXXXPRXXRTATXAYNVTXAFGRRGPEXTXGNFGDXELIRXGTDYKH +WPXIAXFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY +KTFPPTEPXXDXXXXADETXALPXRXXXXXTVTLLPAADLDDFSKXLXXSMSSADSTXA +>tr|A0A663DJA2|A0A663DJA2_9BETC ORF10 protein OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF10 PE=2 SV=1 +MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT +>sp|P0DTD2|ORF9B_WCPV Protein 9b OS=Wuhan seafood market pneumonia virus OX=2697049 PE=3 SV=1 +MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT +LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK +>sp|P0DTD3|Y14_WCPV Uncharacterized protein 14 OS=Wuhan seafood market pneumonia virus OX=2697049 GN=ORF14 PE=3 SV=1 +MLQSCYNFLKEQHCQKASTQKGAEAAVKPLLVPHHVVATVQEIQLQAAVGEXXXXEWXAM +AVMXXXXXXXXTD From 941b5e358844e6f51128e6db94f879bdf177917a Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:30:34 +0300 Subject: [PATCH 06/10] Update README --- DARK/README | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/DARK/README b/DARK/README index c4cf64f..995148a 100644 --- a/DARK/README +++ b/DARK/README @@ -9,3 +9,9 @@ http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. - casttab2swmodel.pl Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. No external dependencies. + +On the command line simply run: +$perl casttab2swmodel.pl path/to/cast_tab_file > path/to/hackathon.tab + +-coronavirus.fasta.CASTV2.2.thr20 +Raw tab output from CAST v2.2. From 9fa86153693d2f7adc43bad4a225d42521c75502 Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:30:55 +0300 Subject: [PATCH 07/10] Rename README to README.md --- DARK/{README => README.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename DARK/{README => README.md} (100%) diff --git a/DARK/README b/DARK/README.md similarity index 100% rename from DARK/README rename to DARK/README.md From 611d4ce0a7d1a395d0a8f69a4d46cc86534173fd Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:34:18 +0300 Subject: [PATCH 08/10] Update README.md --- DARK/README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/DARK/README.md b/DARK/README.md index 995148a..1c02e7b 100644 --- a/DARK/README.md +++ b/DARK/README.md @@ -1,17 +1,17 @@ -Contents of covid-19-Annotations-on-Structures/DARK +Contents of [covid-19-Annotations-on-Structures/DARK](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK) -- coronavirus.fasta.CAST_thr20_4hackathon.tab + +## coronavirus.fasta.CAST_thr20_4hackathon.tab Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. Regions are colored according to amino acid type, following the Rasmol color scheme as described in http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. -- casttab2swmodel.pl -Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. -No external dependencies. +## casttab2swmodel.pl +Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. No external dependencies. On the command line simply run: $perl casttab2swmodel.pl path/to/cast_tab_file > path/to/hackathon.tab --coronavirus.fasta.CASTV2.2.thr20 +## coronavirus.fasta.CASTV2.2.thr20 Raw tab output from CAST v2.2. From 2cefda7f6d791703474aa74081e452591ca263dd Mon Sep 17 00:00:00 2001 From: Vasilis J Promponas <49338525+vprobon@users.noreply.github.com> Date: Sat, 11 Apr 2020 14:36:20 +0300 Subject: [PATCH 09/10] Update README.md --- DARK/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/DARK/README.md b/DARK/README.md index 1c02e7b..dab4dd5 100644 --- a/DARK/README.md +++ b/DARK/README.md @@ -1,17 +1,17 @@ -Contents of [covid-19-Annotations-on-Structures/DARK](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK) +## Contents of [covid-19-Annotations-on-Structures/DARK](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK) -## coronavirus.fasta.CAST_thr20_4hackathon.tab +### [coronavirus.fasta.CAST_thr20_4hackathon.tab](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab) Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. Regions are colored according to amino acid type, following the Rasmol color scheme as described in http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. -## casttab2swmodel.pl +### [casttab2swmodel.pl](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/casttab2swmodel.pl) Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. No external dependencies. On the command line simply run: $perl casttab2swmodel.pl path/to/cast_tab_file > path/to/hackathon.tab -## coronavirus.fasta.CASTV2.2.thr20 +### [coronavirus.fasta.CASTV2.2.thr20] (https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/casttab2swmodel.pl) Raw tab output from CAST v2.2. From f32caa705be0e676b06d180678dcfe2916263c2a Mon Sep 17 00:00:00 2001 From: Gerardo Tauriello Date: Sat, 11 Apr 2020 15:10:02 +0200 Subject: [PATCH 10/10] Update README.md --- DARK/README.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/DARK/README.md b/DARK/README.md index dab4dd5..7220cfe 100644 --- a/DARK/README.md +++ b/DARK/README.md @@ -1,17 +1,16 @@ -## Contents of [covid-19-Annotations-on-Structures/DARK](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK) +## Contents of this folder - -### [coronavirus.fasta.CAST_thr20_4hackathon.tab](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/coronavirus.fasta.CAST_thr20_4hackathon.tab) +### [coronavirus.fasta.CAST_thr20_4hackathon.tab](./coronavirus.fasta.CAST_thr20_4hackathon.tab) Compositionally biased regions detected by the CAST algorithm (Promponas et al., 2000). -CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be inline with the Swiss-Model annotation format. +CAST v2.2 (Ioannides et al., in preparation) tab-separated output, reformatted to be in line with the Swiss-Model annotation format. Regions are colored according to amino acid type, following the Rasmol color scheme as described in http://life.nthu.edu.tw/~fmhsu/rasframe/SHAPELY.HTM. -### [casttab2swmodel.pl](https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/casttab2swmodel.pl) +### [casttab2swmodel.pl](./casttab2swmodel.pl) Perl code to reformat CAST output for input to Swiss-Model portal. Tested with perl v5.16.2 on MacOS, should work fine on Linux/Windows as well. No external dependencies. On the command line simply run: $perl casttab2swmodel.pl path/to/cast_tab_file > path/to/hackathon.tab -### [coronavirus.fasta.CASTV2.2.thr20] (https://github.com/gtauriello/covid-19-Annotations-on-Structures/tree/master/DARK/casttab2swmodel.pl) -Raw tab output from CAST v2.2. +### [coronavirus.fasta.CASTV2.2.thr20](./coronavirus.fasta.CASTV2.2.thr20) +Raw tab output from CAST v2.2 to be used for Perl script above.