DAVI accepts three types of input files:

1) Protein sequences in FASTA format (max 200 sequences)- Download it
>scherichia_coli_strain K12 MPEQYRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPH SFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRD PEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPD LAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIG QPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFE TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKF KDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAI GHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLG EEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEG NEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENAIA >Candidatus_Omnitrophica MSKSLRNRILIILGVIAAAVYFTFPVEKHLNLGLDLKGGMHLVLKVDTEKLPENARQDAVLRAIEILRNRIDGMGVAETVIQRQGETEILVQLPGVTDRDAALAMVGKVAQLEFRLVDDD PGRLKSALEGNVPQGFLLKNVKEKEREPVLLEDQVALGGERISDARVDFDTQGFGQPYISITLNNEGAAEFANLTKTNVGRRLAILLDGEVLSAPNIREAILGGSAQITGQFTLDEASLL SLALRSGALPAPMHVEEERTIGPLLGKDSIEAGINATRIGASLVFLFMVLYYIKAGFIADIALLINLLLIFGTMGFLSIMLPENRLTLTLPGIAGIILTLGMAVDANVLINERIREEIKN GRTIQAAINSGFSRALSAIIDSNATTLIAAFMLFQFGSGPIKGFAVTLTIGLLTSLFTALFVSRTLFNIAYNLGLMQKLPMLSLWSNSKIDFLTFPKRTFAFALSTGLIIVTVMTMAQKK DAAYGIDFVGGQIQEYKFSRPVEVERLREGLRNAGVEAIIQQFDQAPEVVMIRSSADTYEKVSQEFRNRFPENKFEILRIENVGXPRAREHAQARAQEPARDHQRKYQPDVKPHHIDDLR HRPGRCGVVFLRRRGPQHLCLVPDDRVRGGNVFDGLYRLAHRAGVAKEEVNVMFQAVELFVDKILAPDELVRTIADLRYRRVNRVMEQGEFSQRGSIVDIYPADFDAPLRVDLENDHVRS IATINSQTGRPIWQHKIVIILPARAAGGPNKPSGREVFSADVPLNNFLELQKGDYVVHNNHGIGRYLGIEPVDVAHGKKEHMVIGYRGDDKLFVPVHDMHLVQKYVGFQKKPPRLYPLGS KEWKRVRALIQKRLQRLAAELLHAQAARASLKGFAFSPDVDWQEEFEKKFPFEETPDQTKAALEVKKDMESVRPMDRLLCGDVGYGKTEVALRAAFKAVMDNKQVVVLVPTTILAEQHHY NFSNRLKDFPVKVAMLSRFRTRGEQTAILKELREGGVDIVIGTHRLLSKDIAFKDIGLIIIDEEQRFGVRAKERLKQFRLLADVLMLTATPIPRTLYMALTGVRDMSVIATPPQSRIPVK TGIVEFDEELIQSAIDRELKRKGQVFFLHNRVEDIERIAKIIARLVPRARIGIAHGQMSAHELEEIMLKFLKGMVDVLVCTTIIESGIDVPNANTLIVNRADRFGLSDLHQLRGRVGRFT HKAYAYFIIPSRGQLSIQAKARIEAIEKHSGLGAGFQIAFEDLQIRGAGNILGQEQHGYIATIGFDLYCRLLKESVEHLKKEMAGRELAKGAGTTHGSLN

2) hmmscan output - Download it
This file can be obtained after runing hmmscan program on Pfam database (max 10K lines)
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord # target name accession tlen query name qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- SNF2_N PF00176.23 350 Agaricus_bisporus - 2275 5.3e-15 55.0 0.2 1 2 2.1e-15 5.5e-12 45.1 0.0 2 155 1251 1395 1251 1438 0.77 SNF2 family N-terminal domain SNF2_N PF00176.23 350 Agaricus_bisporus - 2275 5.3e-15 55.0 0.2 2 2 0.00066 1.7 7.3 0.1 179 237 1718 1773 1698 1900 0.60 SNF2 family N-terminal domain DNA_methylase PF00145.17 335 Agaricus_bisporus - 2275 6.8e-13 48.7 3.3 1 4 5.7e-16 1.5e-12 47.6 0.0 21 196 270 454 242 615 0.68 C-5 cytosine-specific DNA methylase DNA_methylase PF00145.17 335 Agaricus_bisporus - 2275 6.8e-13 48.7 3.3 2 4 2.7 6.8e+03 -3.9 0.2 200 235 1461 1495 1413 1548 0.47 C-5 cytosine-specific DNA methylase DNA_methylase PF00145.17 335 Agaricus_bisporus - 2275 6.8e-13 48.7 3.3 3 4 0.95 2.4e+03 -2.5 0.1 184 256 1649 1719 1624 1754 0.72 C-5 cytosine-specific DNA methylase DNA_methylase PF00145.17 335 Agaricus_bisporus - 2275 6.8e-13 48.7 3.3 4 4 0.44 1.1e+03 -1.4 1.1 195 298 1919 2029 1857 2032 0.43 C-5 cytosine-specific DNA methylase Helicase_C PF00271.31 111 Agaricus_bisporus - 2275 6.2e-07 29.8 0.2 1 2 0.12 3e+02 1.8 0.0 16 85 1307 1387 1299 1400 0.73 Helicase conserved C-terminal domain Helicase_C PF00271.31 111 Agaricus_bisporus - 2275 6.2e-07 29.8 0.2 2 2 7.7e-09 2e-05 24.9 0.0 2 111 2129 2245 2128 2245 0.76 Helicase conserved C-terminal domain

2) Domain architecture output - Download it (max 1000 lines)
You can provide domain architectures obtained by any tool, please use DAMA format that contains one protein per line, see bellow how to convert DAMA output
scherichia_coli_strain 1148 PF17757 1.5e-28 129 217 PF02559 2.6e-28 477 572 PF00270 6.1e-24 602 762 PF00271 5.9e-21 803 906 PF03461 3e-31 1006 1098 Candidatus_Omnitrophica 1300 PF02355 3.5e-20 255 427 PF17757 1.2e-19 658 744 PF02559 2.7e-25 770 863 PF00270 4.6e-19 915 1052 PF00271 5.8e-19 1097 1199 Exophiala_dermatitidis 1690 PF13892 6.8e-51 570 701 PF00176 9e-68 833 1122 PF00271 1.2e-22 1403 1515 Capronia_epimyces_CBS 1572 PF13892 4.6e-51 450 581 PF00176 7.3e-68 712 1001 PF00271 1.5e-22 1282 1394 Cladophialophora_yegresii 1499 PF13892 4.1e-51 368 499 PF00176 5.3e-68 631 919 PF00271 2.3e-22 1208 1320 Pseudomonas_aeruginosa 691 PF17191 4.1e-17 12 170 PF00270 9.7e-21 293 430 PF00271 7.1e-19 479 586 Mycobacterium_tuberculosis 737 PF17191 2e-10 20 136 PF00270 6.7e-21 292 464 PF00271 6.6e-22 508 628 Escherichia_coli_O157 693 PF17191 2.4e-23 15 171 PF00270 2.7e-22 273 433 PF00271 4.6e-20 481 588 Bacillus_subtilis_168 682 PF17191 2.7e-20 9 165 PF00270 3.9e-22 260 415 PF00271 2.1e-23 452 572

#Run the below command in the terminal, replace [DAMA_INPUT_FILE] and [DAMA_OUTPUT_FILE] with your files
ramtmp="$(mktemp -p /dev/shm/)"; awk -F '\t' '{if (p == $4) {toPrint=toPrint"\t"$5" "$1" "$2" "$3} else {p = $4; print toPrint; toPrint=$4"\t"$5" "$1" "$2" "$3}} END {print toPrint}' [DAMA_OUTPUT_FILE] > $ramtmp; awk -F'\t' 'NR==FNR{a[$4]=$10;next}{$1=$1"\t"a[$1]; print $0}' [DAMA_INPUT_FILE] $ramtmp | tail -n +2 | tr ' ' '\t' > DamaArchs.txt