A biological signature based method to batch analyze functional similarities of proteins
Duo is a workflow to batch analyze functional similarities of proteins. A key utility provided by Duo is to screen for query proteins with specific characteristics based on highly free and customizable reference protein sequences inputted by users.
- python 3.6.9 and following librarires are required:
- Overview of Duo workflow. (A) A schematic to illustrate the general working processes and the three main input contents defined by users. (B) A schematic to illustrate the correction analysis step between Query_proteins/Reference_proteins and Seed_database. (C) A schematic to illustrate the correction analysis step between Query_proteins and Reference_proteins.
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Query_proteins: query protein sequences file in fasta format
>unknown_protein_1 MARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDF VNVIQGDATLNQALIKDKRTENLFILPASQTRDKDALTREGVAKVLDSLKAMDFEFIVCD SPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLL TRYNPGRVNKGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDATADAGKAYA >unknown_protein_2 MERITVTLGERSYPITIAAGLFNEPASFLPLKSGDQVMLVTNETLAPLYLDKVRGVLERA GVNVDSVILPDGEQYKSLTVLDTVFTALLKKPHGRDTTLVALGGGVIGDLTGFAAASYQR GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPARELAS GLAEVIKYGIILDADFFTWLEGNLDALLRLDGPAMAYCIRRCCELKAEVVAADEREAGLR ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGIVMAARASERLGQFSSTDTQRIIALLERA GLPVNGPCEMSAQDYLPHMLRDKKVLAGELRLVLPLAIGKSEVRGGVSHEVVLSAIADCQ ... -
Reference_proteins: reference protein sequences file in fasta format
>reference_protein_1 MSDDMSMGSPSSAGEQGVLRSMQEVAMSSQEASKMLRTYNIAWWGNNYYDVNELGHISVC PDPDVPEARVDLAKLVKAREAQGQRLPALFCFPQILQHRLRSINAAFKRARESYGYNGDY FLVYPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYI RLALIGEKMGHKVYLVIEKMSEIAIVLEEAERLNVGPRLGVRARLASQGSGKWQSSGGEK SKFGLAATQVLQLVETLRDAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKL GVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDACEEHGLPHPTMITE SGRAVTAHHTVLVSNIIGVERNEYTDPTAPAEDAPRALQNLWETWQEMHKPGTRRSLREW LHDSQMDLHDIHIGYSSGAFSLQERAWAEQLYLSMCHEVQKQLDPQNRAHRPIIDELQER MADKMYVNFSLFQSMPDAWGIDQLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDG DGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGDTEAVDVFVFPDGSVEVELS DEGDTVADMLQYVQLDPKTLLTHFRDQVKQTDLDDALQQQFLEEFEAGLYGYTYLEDE >reference_protein_2 MRRITPFFPFFVLLVSHFSLAISYPLPPEGSRLVGQPVTIAVPQNNTQPLESFAARYGQG LSNMLEANPGVDVFLPQSGSTLVVPQQLILPDTVREGIVVNVAEMRLYYYPAGTNTVEVL PIGIGQAGRGTPRNWVTAVERKQDGPVWVPTANTRREYAKEGKTLPAMVPAGPDNPMGLY AIYIGRLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDHVPVGTRVQIIDRPVKFSVE PDGSRWLEVHEPLSRNRAEFESDKKVPLPVTPVLRTFIKGDDVDTSRVNEVLERRSGMPV NISAGRPGL ... -
Seed_database: protein signatures saved in specific format according the modeling method they applied.
For example: HMMs profile
HMMER3/f [3.3.1 | Jul 2020]
NAME globins4
LENG 149
ALPH amino
RF no
MM no
CONS yes
CS no
MAP yes
DATE Tue Jul 21 10:15:03 2020
NSEQ 4
EFFN 0.964844
CKSUM 2027839109
STATS LOCAL MSV -9.8664 0.70955
STATS LOCAL VITERBI -10.7223 0.70955
STATS LOCAL FORWARD -4.1641 0.70955
HMM A C D E F G H ... W Y
m->m m->i m->d i->m i->i d->m d->d
COMPO 2.36800 4.52198 2.96929 2.70577 3.20715 3.01836 3.40293 ... 4.55599 3.63079
2.68638 4.42245 2.77499 2.73143 3.46374 2.40505 3.72514 ... 4.58497 3.61523
0.55970 1.87270 1.29132 1.73023 0.19509 0.00000 *
1 1.75819 4.17850 3.77264 3.37715 3.71018 3.31297 4.28273 ... 5.32308 4.09587 9 v - - -
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 ... 4.58477 3.61503
0.03182 3.85936 4.58171 0.61958 0.77255 0.34183 1.23951
...
149 2.93078 5.12630 3.29219 2.66308 4.49202 3.60568 2.46960 ... 5.42994 4.19803 165 k - - -
2.68634 4.42241 2.77535 2.73098 3.46370 2.40469 3.72510 ... 4.58493 3.61420
0.21295 1.65128 * 1.49930 0.25268 0.00000 *
//
...
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domain_correlation.csv: tab-delimited text file, details all the correlation records among Query_proteins, Reference_proteins and Seed_database
- Example of domain_correlation.csv output from domain_correlation.InterPro.py
ACC DB DESCRIPTION HIT_PROTEINS(name,domain_num)_R HIT_PROTEINS_R HIT_PROTEINS_NUM_R HIT_PROTEINS(name,domain_num)_Q HIT_PROTEINS_Q HIT_PROTEINS_NUM_Q
0 G3DSA:1.10.10.10 GENE3D <unknown description> ('VFG042447(gb|AAA23662)', 1);('VFG042390(gb|YP_540132)', 1);('VFG042429(gb|CAA54112)', 1);('VFG000880(gb|NP_755468)', 1);('VFG002413(gb|NP_286011)', 1);('VFG042440(gb|AAK16195)', 1);('VFG001713(gb|NP_755457)', 1);('VFG012327(gb|YP_540122)', 1) VFG042447(gb|AAA23662);VFG042390(gb|YP_540132);VFG042429(gb|CAA54112);VFG000880(gb|NP_755468);VFG002413(gb|NP_286011);VFG042440(gb|AAK16195);VFG001713(gb|NP_755457);VFG012327(gb|YP_540122) 8.0 ('STM0960', 1);('STM0068', 1);('STM3876', 1);('STM1547', 1);('STM1805', 1);('STM4588', 1);('STM3682', 2);('STM3888', 1);('STM2920', 1);('STM2145', 1);('STM3014', 1);('STM1127', 1);('STM1950', 1);('STM2275', 1);('STM0115', 1);('STM1625', 1);('STM3533', 1);('STM1887', 1);('STM0347', 1);('STM2557', 1);('STM1523', 1);('STM2131', 1);('STM1894', 1);('STM1842', 1);('STM4270', 1);('STM1659', 1);('STM0466', 1);('STM1520', 1);('PSLT013', 1);('STM3064', 1);('STM0397', 1);('STM0789', 1);('STM3124', 1);('STM2201', 1);('STM1096', 1);('STM3215', 1);('STM1598', 1);('STM3507', 1);('STM0459', 1);('STM3958', 1);('STM2069', 1);('STM3502', 1);('STM0151', 1);('STM1677', 1);('STM2373', 1);('STM4138', 1);('STM2982', 1);('STM2837', 1);('STM0693', 1);('STM2924', 2);('PSLT012', 1);('STM3405', 1);('STM2455', 1);('STM3367', 1);('STM3211', 2);('STM3667', 1);('STM3466', 1);('STM2803', 1);('STM2281', 1);('STM1541', 1);('STM0835', 1);('STM4237', 1);('STM2572', 1);('STM3084', 1);('STM0430', 1);('STM2420', 1);('STM4507', 1);('STM4068', 1);('STM4073', 1);('STM0410', 1);('STM0606', 1);('STM4448', 1);('STM3262', 1);('STM0702', 1);('STM3177', 1);('STM0514', 1);('STM3693', 1);('STM3759', 1);('STM0779', 1);('STM3607', 1);('STM0952', 1);('STM0763', 1);('STM1014', 1);('STM4241', 1);('STM0030', 1);('STM0040', 1);('STM0959', 1);('STM2270', 1);('STM3848', 1);('STM1429', 1);('STM3357', 1);('STM1767', 1);('STM3360', 1);('STM1713', 1);('STM3121', 1);('STM2813', 1);('STM3252', 1);('STM0516', 1);('STM2544', 1);('STM2794', 1);('STM2912', 1);('STM4125', 1);('STM2609', 1);('STM2575', 1);('STM0992', 1);('STM4337', 1);('STM3964', 1);('STM2828', 3);('STM1660', 1);('STM0634', 1);('STM1487', 1);('STM3830', 1);('STM4417', 1);('STM4548', 1);('STM1001', 1);('STM4292', 1);('STM3020', 1);('STM1142', 1);('STM0017', 1);('STM2979', 1);('STM4059', 1);('STM0029', 1);('STM1265', 1);('STM2330', 1);('STM4367', 1);('STM3523', 1);('STM3736', 1);('STM4187', 1);('STM3547', 1);('STM1704', 1);('STM1231', 1);('STM2292', 1);('STM2797', 1);('STM3358', 1);('STM3235', 1);('STM0031', 1);('STM3908', 1);('STM2424', 1);('STM0682', 1);('STM2640', 1);('STM2644', 1);('STM0014', 1);('STM3098', 1);('STM1510', 1);('STM1382', 1);('STM3785', 1);('STM0256', 1);('STM2876', 1);('STM2919', 1);('STM1444', 1);('STM0552', 1);('STM4463', 1);('STM3602', 1);('STM0344', 1);('STM0859', 1);('STM3824', 1);('STM3340', 1);('STM2180', 1);('STM1168', 2);('STM3800', 1);('STM1588', 1);('STM3834', 1);('STM4025', 1);('STM2265', 1);('STM0304', 1);('STM3515', 1);('STM3245', 1);('STM2436', 1);('STM4598', 1);('STM1475', 1);('STM1982', 1);('STM1488', 1);('STM1100', 1);('PSLT041', 1);('STM3897', 1);('STM4511', 1);('STM3606', 1);('STM0764', 1);('STM4314', 1);('STM0333', 1);('STM2785', 1);('STM1387', 1);('STM0692', 1);('STM4402', 1) STM0960;STM0068;STM3876;STM1547;STM1805;STM4588;STM3682;STM3888;STM2920;STM2145;STM3014;STM1127;STM1950;STM2275;STM0115;STM1625;STM3533;STM1887;STM0347;STM2557;STM1523;STM2131;STM1894;STM1842;STM4270;STM1659;STM0466;STM1520;PSLT013;STM3064;STM0397;STM0789;STM3124;STM2201;STM1096;STM3215;STM1598;STM3507;STM0459;STM3958;STM2069;STM3502;STM0151;STM1677;STM2373;STM4138;STM2982;STM2837;STM0693;STM2924;PSLT012;STM3405;STM2455;STM3367;STM3211;STM3667;STM3466;STM2803;STM2281;STM1541;STM0835;STM4237;STM2572;STM3084;STM0430;STM2420;STM4507;STM4068;STM4073;STM0410;STM0606;STM4448;STM3262;STM0702;STM3177;STM0514;STM3693;STM3759;STM0779;STM3607;STM0952;STM0763;STM1014;STM4241;STM0030;STM0040;STM0959;STM2270;STM3848;STM1429;STM3357;STM1767;STM3360;STM1713;STM3121;STM2813;STM3252;STM0516;STM2544;STM2794;STM2912;STM4125;STM2609;STM2575;STM0992;STM4337;STM3964;STM2828;STM1660;STM0634;STM1487;STM3830;STM4417;STM4548;STM1001;STM4292;STM3020;STM1142;STM0017;STM2979;STM4059;STM0029;STM1265;STM2330;STM4367;STM3523;STM3736;STM4187;STM3547;STM1704;STM1231;STM2292;STM2797;STM3358;STM3235;STM0031;STM3908;STM2424;STM0682;STM2640;STM2644;STM0014;STM3098;STM1510;STM1382;STM3785;STM0256;STM2876;STM2919;STM1444;STM0552;STM4463;STM3602;STM0344;STM0859;STM3824;STM3340;STM2180;STM1168;STM3800;STM1588;STM3834;STM4025;STM2265;STM0304;STM3515;STM3245;STM2436;STM4598;STM1475;STM1982;STM1488;STM1100;PSLT041;STM3897;STM4511;STM3606;STM0764;STM4314;STM0333;STM2785;STM1387;STM0692;STM4402 184.0
1 PF04703 PFAM FaeA-like protein ('VFG042447(gb|AAA23662)', 1);('VFG042429(gb|CAA54112)', 1);('VFG000880(gb|NP_755468)', 1);('VFG042440(gb|AAK16195)', 1);('VFG012327(gb|YP_540122)', 1) VFG042447(gb|AAA23662);VFG042429(gb|CAA54112);VFG000880(gb|NP_755468);VFG042440(gb|AAK16195);VFG012327(gb|YP_540122) 5.0 ('PSLT013', 1) PSLT013 1.0
2 ...
Content Name: Explanation
AAC: accession number(id) of the matched biological entity in Seed_database.
DB: the member Seed_database name applied in InterProscan.
DESCRIPTION: the annotation information of the matched biological entity.
HIT_PROTEINS(name,domain_num)_R: records the protein name and the domain number to the matched biological entity in Reference_proteins.
HIT_PROTEINS_R: records the protein name to the matched biological entity in Reference_proteins.
HIT_PROTEINS_NUM_R: count the protein number to the matched biological entity in Reference_proteins.
HIT_PROTEINS(name,domain_num)_Q: records the protein name and the domain number to the matched biological entity in Query_proteins.
HIT_PROTEINS_Q: records the protein name to the matched biological entity in Query_proteins.
HIT_PROTEINS_NUM_Q: count the protein number to the matched biological entity in Query_proteins.
-
domain_correlation_inner.csv: subset of domain_correlation.csv file who only details the correlation records shared between Query_proteins and Reference_proteins.
-
HITPROTEINS: a folder who contains the detailed protein names that correlated between Reference_proteins and Query_proteins.
- Example of one output file in HITPROTEINS folder (PFAM_HITPROTEINS_Q)
STM1091
STM2897
STM1412
STM0301
STM4572
STM2150
STM3028
STM0175
STM3638
STM0023
PSLT017
...
- INPUT_BACKUP: a folder who contains the copys of the Query_proteins and Reference_proteins files inputted by user.
- This is a hmmer3 dependent python script to correlate the proteins (references proteins/query proteins) according the pfam database (or other HMMs_profile)
Usage: pyhont3 domain_correlation_hmmer3.py
--Q_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Query_proteins")
--R_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Reference_proteins")
--HMMDB_PATH (required=True, type=str, metavar='PATH', help="the path of hmm profile database (Seed_database). eg. /home/fix/downloads/pfam.hmmlib")
--OUTPUT (default="domain_cor_hmmer3", type=str, metavar='directory', help="Output directory name")
--PFAM (action='store_const', const=True, metavar='add --cut_tc option in hmmscan specific for pfam_db', help="optional, specific designed for pfam_db")
--CPU (default=1, type=int, metavar='the cpu num you want to use', help="the cup number you want to use during hmmscan process, default is 1")
--HIT_EVALUE (default=0.001, type=int, metavar='evalue thread', help="the evalue thread use during extracting hmm profile in domain-table, default is 0.001")
--BIT_SCORE (default=10, type=int, metavar='bitscore thread', help="the bitscore thread use during extracting hmm profile in domain-table, default is 10")
- This is a ps_scan dependent python script to correlate the proteins (references proteins/query proteins) according the scanProsite database.
Usage: python3 domain_correlation_prosite.py
--Q_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Query_proteins")
--R_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Reference_proteins")
--PROSITE_DB_PATH (required=True, type=str, metavar='PATH', help="the path of prosite.dat profile (Seed_database). eg. /home/fix/downloads/prosite.dat")
--EVALUATOR_PATH (required=True, type=str, metavar='PATH', help="the path of evaluator.dat profile (for evaluate the pattern). eg. /home/fix/downloads/evaluator.dat")
--ps_scan_PATH (required=True, type=str, metavar='PATH', help="the folder path of ps_scan.pl program. eg. /home/fix/ps_scan/")
--OUTPUT (default="domain_cor_prosite", type=str, metavar='directory', help="Output directory name")
--ONLY_DOM (action='store_const', const=True, metavar='ONLY_DOMMAIN_DB', help="optional,only ps_scan the protein domain profiles")
--ONLY_PAT (action='store_const', const=True, metavar='ONLY_PATTERN_DB', help="optional,only ps_scan the protein pattern profiles")
--SIMPLE_ANN (action='store_const', const=True, metavar='ONLY SHOW THE MATCH ACC', help="optional, in the ouput only show the match profile ID, without detail description")
- This is a InterProScan dependent python script to correlate the proteins (references proteins/query proteins) according the different member databases.
Usage: python3 domain_correlation_InterPro.py
--Q_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Query_proteins")
--R_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file as Reference_proteins")
--INTERPROSCAN_BIN (required=True, type=str, metavar='PATH', help="the path of hmm profile InterProScan. eg. /home/fix/export_bin/InterProScan/interproscan-5.46-81.0/interproscan.sh")
--OUTPUT (default="domain_cor_InterPro", type=str, metavar='directory', help="Output directory name")
- This is a hmmer3 dependent python script to constract your own customed pfam profiles database according the proteins you feed to the total pfam databse
Usage: python3 custom_pfamdb.py
--CUSTOM_PROTEINS (required=True, type=str, metavar='FILENAME', help="the user selected proteins file (Reference_proteins) to help construct the custom_pfam databse")
--HMMDB_PATH (required=True, type=str, metavar='PATH', help="the path of hmm profile database. eg. /home/fix/downloads/pfam.hmmlib")
--OUTPUT (default="custom_pfamdb_out", type=str, metavar='directory', help="Output directory name")
--DETAIL_DIC (action='store_const', const=True, metavar='get detailed hmms dictornary', help="optional, get more detailed hmms dictorynary")
--CPU (default=1, type=int, metavar='the cpu num you want to use', help="the cup number you want to use during hmmscan process, default is 1")
--HIT_EVALUE (default=0.001, type=int, metavar='evalue thread', help="the evalue thread use during extracting hmm profile in domain-table, default is 0.001")
--BIT_SCORE (default=10, type=int, metavar='bitscore thread', help="the bitscore thread use during extracting hmm profile in domain-table, default is 10")
Fei, X., Li, Q., Olsen, J. E., & Jiao, X. (2021). Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. Frontiers in microbiology, 2308.
This study was supported by the National Natural Science Foundation of China (31730094 and 31920103015). XF was supported by funding from the China Scholarship Council (201808320379) and Postgraduate Research &Practice Innovation Program of Jiangsu Province（Yangzhou University）(XKYCX18_102).