Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives.
bioinformatics
biotechnological applications
marine observatories
marine resources
omics
Journal
Marine drugs
ISSN: 1660-3397
Titre abrégé: Mar Drugs
Pays: Switzerland
ID NLM: 101213729
Informations de publication
Date de publication:
11 Oct 2019
11 Oct 2019
Historique:
received:
20
08
2019
revised:
01
10
2019
accepted:
02
10
2019
entrez:
17
10
2019
pubmed:
17
10
2019
medline:
28
2
2020
Statut:
epublish
Résumé
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
Identifiants
pubmed: 31614509
pii: md17100576
doi: 10.3390/md17100576
pmc: PMC6835618
pii:
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Références
Nat Methods. 2014 Feb;11(2):122-3
pubmed: 24481216
Nat Commun. 2019 Apr 23;10(1):1822
pubmed: 31015394
Appl Environ Microbiol. 2019 Apr 4;85(8):
pubmed: 30737349
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Nucleic Acids Res. 2016 Jan 4;44(D1):D48-50
pubmed: 26657633
Biochim Biophys Acta Gen Subj. 2020 Feb;1864(2):
pubmed: 31302180
Nat Methods. 2017 Oct 31;14(11):1023-1024
pubmed: 29088129
BMC Genomics. 2018 May 24;19(1):394
pubmed: 29793428
J Chem Theory Comput. 2008 Mar;4(3):435-47
pubmed: 26620784
Front Microbiol. 2018 Jun 20;9:1235
pubmed: 29973918
Int J Mol Sci. 2018 Dec 05;19(12):
pubmed: 30563163
Science. 2004 Apr 2;304(5667):66-74
pubmed: 15001713
J Biotechnol. 2017 Nov 10;261:137-141
pubmed: 28554829
Adv Food Nutr Res. 2017;80:75-106
pubmed: 28215329
Anal Chem. 2017 Mar 21;89(6):3318-3325
pubmed: 28233997
Chem Biol Drug Des. 2019 Jan;93(1):12-20
pubmed: 30187647
PLoS Comput Biol. 2009 Jan;5(1):e1000262
pubmed: 19148271
Nucleic Acids Res. 2012 Jan;40(Database issue):D54-6
pubmed: 22009675
Brief Bioinform. 2013 Mar;14(2):131-43
pubmed: 22764121
Science. 1991 Jul 12;253(5016):164-70
pubmed: 1853201
Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3817-22
pubmed: 9108061
F1000Res. 2017 Jan 23;6:
pubmed: 28620454
Sci Data. 2018 Jan 16;5:170203
pubmed: 29337314
BMC Plant Biol. 2015 Feb 13;15:48
pubmed: 25849067
Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4
pubmed: 25845596
PLoS One. 2012;7(3):e34064
pubmed: 22479523
Trends Ecol Evol. 2019 Nov;34(11):1022-1033
pubmed: 31350054
Pak J Pharm Sci. 2019 May;32(3 (Supplementary)):1253-1259
pubmed: 31303598
Nucleic Acids Res. 2019 Jan 8;47(D1):D745-D751
pubmed: 30407521
Nat Rev Microbiol. 2014 Oct;12(10):699-713
pubmed: 25157695
Bioinformatics. 2009 Jan 15;25(2):288-9
pubmed: 19033274
Sci Data. 2018 Oct 08;5:180197
pubmed: 30295671
Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199
pubmed: 27899635
Genome Res. 2017 Jan;27(1):133-144
pubmed: 28003436
Sci Rep. 2017 Mar 13;7:44230
pubmed: 28287181
Stand Genomic Sci. 2011 Dec 31;5(3):424-9
pubmed: 22675592
BMC Bioinformatics. 2015 Mar 12;16:79
pubmed: 25888166
F1000Res. 2017 Jul 19;6:1148
pubmed: 28781759
Int J Biol Macromol. 2019 Jun 15;131:536-547
pubmed: 30885732
Drug Metabol Drug Interact. 2012;27(4):199-207
pubmed: 23152402
Annu Rev Genet. 2005;39:309-38
pubmed: 16285863
Sci Adv. 2016 Apr 29;2(4):e1500961
pubmed: 27386507
Mar Environ Res. 2017 Jul;128:58-69
pubmed: 27160988
Nucleic Acids Res. 2017 Jan 4;45(D1):D529-D534
pubmed: 28053165
Proc Biol Sci. 2014 Feb 12;281(1780):20133299
pubmed: 24523277
Curr Opin Biotechnol. 2019 Feb;55:44-50
pubmed: 30138778
Sci Rep. 2018 Sep 10;8(1):13553
pubmed: 30202061
Nat Methods. 2008 May;5(5):405-7
pubmed: 18425140
J Evol Biol. 2005 Jul;18(4):901-10
pubmed: 16033562
Toxins (Basel). 2019 Jun 25;11(6):
pubmed: 31242582
Fish Shellfish Immunol. 2019 Mar;86:1177-1193
pubmed: 30599257
Molecules. 2016 Jul 08;21(7):
pubmed: 27399665
Genes (Basel). 2010 Sep 14;1(2):294-307
pubmed: 24710047
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Curr Opin Biotechnol. 2012 Aug;23(4):609-16
pubmed: 22153034
Nucleic Acids Res. 2010 Jan;38(Database issue):D33-8
pubmed: 19850725
Nucleic Acids Res. 2018 Jul 2;46(W1):W289-W295
pubmed: 29788376
Bioresour Technol. 2016 Feb;202:244-52
pubmed: 26724870
J Proteomics. 2009 Mar 6;72(2):210-8
pubmed: 19457347
Pharmacol Res. 2019 Sep;147:104373
pubmed: 31351913
Brief Funct Genomic Proteomic. 2009 Jan;8(1):75-87
pubmed: 19279070
J Proteomics. 2011 Jun 10;74(7):920-34
pubmed: 21477672
BMC Bioinformatics. 2008 Sep 19;9:386
pubmed: 18803844
Nat Commun. 2018 Nov 27;9(1):4999
pubmed: 30479325
Curr Opin Plant Biol. 2005 Apr;8(2):135-41
pubmed: 15752992
Methods Mol Biol. 2012;855:259-79
pubmed: 22407712
Biophys Rev. 2017 Apr;9(2):91-102
pubmed: 28510083
Nat Rev Genet. 2009 Oct;10(10):669-80
pubmed: 19736561
PLoS Biol. 2007 Mar;5(3):e85
pubmed: 20076663
Trends Ecol Evol. 2005 Jun;20(6):312-9
pubmed: 16701387
Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85
pubmed: 15590779
Science. 2006 Nov 10;314(5801):941-52
pubmed: 17095691
Sci Rep. 2017 May 8;7(1):1562
pubmed: 28484228
Bioinform Biol Insights. 2017 Feb 23;11:1177932217690136
pubmed: 28469416
Mar Drugs. 2017 Mar 30;15(4):
pubmed: 28358320
Anal Chem. 2015 Mar 17;87(6):3129-33
pubmed: 25719549
Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11121-E11130
pubmed: 29229817
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Curr Biol. 2009 Jul 28;19(14):R602-14
pubmed: 19640499
Curr Opin Biotechnol. 2018 Apr;50:111-120
pubmed: 29232601
Genome Biol. 2019 May 16;20(1):92
pubmed: 31097009
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Trends Pharmacol Sci. 2003 Aug;24(8):434-9
pubmed: 12915054
Curr Opin Microbiol. 2015 Feb;23:148-54
pubmed: 25483351
ACS Chem Biol. 2015 Dec 18;10(12):2841-2849
pubmed: 26458099
Adv Food Nutr Res. 2017;80:181-197
pubmed: 28215326
Nat Rev Genet. 2013 May;14(5):360-6
pubmed: 23552219
BMC Genomics. 2012 Jun 28;13:284
pubmed: 22742208
Acta Crystallogr D Biol Crystallogr. 1999 Mar;55(Pt 3):583-601
pubmed: 10089455
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Biotechnol Adv. 2011 Sep-Oct;29(5):468-82
pubmed: 21419836
Brief Bioinform. 2012 Nov;13(6):728-42
pubmed: 22966151
J Comput Chem. 2005 Dec;26(16):1781-802
pubmed: 16222654
BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):435
pubmed: 30497367
Adm Policy Ment Health. 2009 Nov;36(6):374-80
pubmed: 19777336
Nucleic Acids Res. 2018 Jan 4;46(D1):D633-D639
pubmed: 29059334
Curr Opin Biotechnol. 2018 Dec;54:1-9
pubmed: 29413745
Neuron. 2018 Sep 19;99(6):1129-1143
pubmed: 30236283
ISME J. 2014 Jul;8(7):1440-51
pubmed: 24451205
Chem Commun (Camb). 2014 Jan 14;50(4):406-8
pubmed: 23963116
ACS Chem Biol. 2017 May 19;12(5):1281-1287
pubmed: 28198609
J Appl Microbiol. 2011 Oct;111(4):787-99
pubmed: 21777355
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W270-7
pubmed: 21624888
Sci Rep. 2019 Mar 4;9(1):3336
pubmed: 30833632
Nucleic Acids Res. 2015 Jan;43(Database issue):D1113-6
pubmed: 25361974
Front Genet. 2017 Mar 06;8:23
pubmed: 28321234
Nucleic Acids Res. 2016 Jan 4;44(D1):D51-7
pubmed: 26578571
FEMS Microbiol Lett. 2005 Jan 1;242(1):127-36
pubmed: 15621429
BMC Genomics. 2010 Nov 16;11:634
pubmed: 21080938
Environ Microbiol Rep. 2016 Aug;8(4):452-60
pubmed: 26991974
Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56
pubmed: 25428369
Nat Prod Rep. 2015 Aug;32(8):1163-4
pubmed: 26155872
Proteins. 2019 Jul;87(7):596-606
pubmed: 30882932
Biodivers Data J. 2016 May 25;(4):e8080
pubmed: 27346955
J Mol Biol. 1970 Mar;48(3):443-53
pubmed: 5420325
Annu Rev Genet. 2007;41:465-507
pubmed: 17678444
BMC Evol Biol. 2016 Jun 29;16(1):142
pubmed: 27356756
Biotechnol Prog. 2015 Jul-Aug;31(4):890-9
pubmed: 25920073
Proteomics. 2001 Aug;1(8):927-33
pubmed: 11683509
Sci China Life Sci. 2013 Feb;56(2):156-62
pubmed: 23393031
J Comput Chem. 2009 Oct;30(13):2021-30
pubmed: 19130502
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Sci Rep. 2017 Sep 15;7(1):11701
pubmed: 28916825
Appl Microbiol Biotechnol. 2015 Mar;99(5):2165-78
pubmed: 25194841
J Proteome Res. 2010 Mar 5;9(3):1323-9
pubmed: 20113005
Mar Drugs. 2018 Jun 13;16(6):
pubmed: 29899267
Curr Top Med Chem. 2017;17(18):2023-2040
pubmed: 28137238
Mar Drugs. 2018 Jun 02;16(6):
pubmed: 29865236
Nat Biotechnol. 2012 Aug;30(8):777-82
pubmed: 22820318
J Comput Chem. 2010 Jan 30;31(2):455-61
pubmed: 19499576
Proteomics. 2014 Oct;14(19):2200-11
pubmed: 25073878
Nucleic Acids Res. 2016 Jan 4;44(D1):D595-603
pubmed: 26582919
Trends Genet. 2002 Dec;18(12):619-20
pubmed: 12446146
Mar Drugs. 2017 Apr 12;15(4):
pubmed: 28417932
Curr Opin Microbiol. 2008 Oct;11(5):472-7
pubmed: 19086349
Epigenomics. 2015;7(8):1287-302
pubmed: 26192535
Front Microbiol. 2015 Aug 28;6:890
pubmed: 26379658
Brief Bioinform. 2016 Sep;17(5):877-90
pubmed: 26454094
Sci Rep. 2018 Jul 5;8(1):10187
pubmed: 29976990
BMC Biol. 2016 Jun 07;14:43
pubmed: 27267928
Mar Drugs. 2018 Jan 24;16(2):
pubmed: 29364843
Appl Biochem Biotechnol. 2017 Oct;183(2):636-651
pubmed: 28815469
Extremophiles. 2000 Apr;4(2):83-90
pubmed: 10805562
Biotechnol Lett. 2010 Oct;32(10):1351-9
pubmed: 20495950
Bioresour Technol. 2019 Nov;291:121932
pubmed: 31387837
BMC Genomics. 2015 Mar 07;16:158
pubmed: 25879706
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7
pubmed: 24861617
Nat Chem Biol. 2015 Sep;11(9):639-48
pubmed: 26284671
Drug Discov Today. 2005 Jul 1;10(13):895-907
pubmed: 15993809
Nucleic Acids Res. 2016 Jan 4;44(D1):D590-4
pubmed: 26656948
PLoS One. 2017 Dec 21;12(12):e0190152
pubmed: 29267363
Sci Rep. 2018 Nov 9;8(1):16600
pubmed: 30413766
New Phytol. 2015 Feb;205(3):1195-210
pubmed: 25354164
Science. 2009 Jul 10;325(5937):161-5
pubmed: 19589993
Nat Biotechnol. 2016 Aug 9;34(8):828-837
pubmed: 27504778
Mar Drugs. 2013 Mar 08;11(3):700-17
pubmed: 23528949
Cell. 2019 May 16;177(5):1109-1123.e14
pubmed: 31031001
Front Microbiol. 2018 Sep 06;9:2072
pubmed: 30237790
Phytochem Anal. 2018 Nov;29(6):543-548
pubmed: 29672972
mSystems. 2018 Jul 10;3(4):
pubmed: 30003143
Nat Genet. 1993 Aug;4(4):332-3
pubmed: 8401577
Nucleic Acids Res. 2018 Jan 4;46(D1):D718-D725
pubmed: 29149270
J Ind Microbiol Biotechnol. 2016 Mar;43(2-3):155-76
pubmed: 26739136
Expert Opin Drug Discov. 2008 Aug;3(8):903-29
pubmed: 23484967
Appl Biochem Biotechnol. 2014 Mar;172(6):3054-68
pubmed: 24488777
Front Microbiol. 2014 Nov 12;5:605
pubmed: 25452749
J Mass Spectrom. 2002 Jul;37(7):663-75
pubmed: 12124999
Mar Pollut Bull. 2013 Sep 15;74(1):19-31
pubmed: 23806673
Int J Syst Evol Microbiol. 2012 May;62(Pt 5):1171-8
pubmed: 21724952
Genes (Basel). 2018 Sep 28;9(10):
pubmed: 30274234
ISME J. 2019 Aug;13(8):2094-2106
pubmed: 31024153
Mar Genomics. 2012 Dec;8:15-22
pubmed: 23199876
Anal Chem. 2011 Sep 15;83(18):7074-80
pubmed: 21830798
Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677
pubmed: 30289528
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Nucleic Acids Res. 2018 Jan 4;46(D1):D692-D699
pubmed: 29106641
Mar Genomics. 2014 Oct;17:35-42
pubmed: 24780860
Science. 2002 Dec 13;298(5601):2157-67
pubmed: 12481130
Mar Genomics. 2018 Feb;37:114-119
pubmed: 28919018
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51
pubmed: 22645317
Curr Issues Mol Biol. 2018;27:71-88
pubmed: 28885175
Proteomics. 2015 Dec;15(23-24):3921-4
pubmed: 26769186
Curr Protoc Bioinformatics. 2014 Dec 12;48:3.13.1-16
pubmed: 25501942
Cold Spring Harb Protoc. 2015 Apr 13;2015(11):951-69
pubmed: 25870306
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
J Mol Biol. 1981 Mar 25;147(1):195-7
pubmed: 7265238
Methods Mol Biol. 2016;1401:209-32
pubmed: 26831711
BMC Genomics. 2017 Jan 13;18(1):76
pubmed: 28086785
Phytochemistry. 2007 Apr;68(7):954-79
pubmed: 17336349
J Proteome Res. 2005 Jul-Aug;4(4):1155-70
pubmed: 16083266
Science. 2015 May 22;348(6237):873
pubmed: 25999501
Annu Rev Biomed Eng. 2009;11:49-79
pubmed: 19400705
Plant Signal Behav. 2016;11(4):e1158381
pubmed: 26950417
Nature. 2018 Mar 7;555(7695):175-182
pubmed: 29517004
Wiley Interdiscip Rev RNA. 2017 Jan;8(1):
pubmed: 27198714
Curr Protoc Bioinformatics. 2017 Sep 13;59:11.15.1-11.15.21
pubmed: 28902396
BMC Res Notes. 2015 Sep 26;8:479
pubmed: 26409790
New Phytol. 2015 Apr;206(1):127-32
pubmed: 25628124
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655
pubmed: 29145629
Science. 2000 Sep 15;289(5486):1902-6
pubmed: 10988064
BMC Genomics. 2017 Jan 17;18(1):93
pubmed: 28095778
Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31
pubmed: 20972220
J Comput Chem. 2011 Jul 30;32(10):2149-59
pubmed: 21541955
Annu Rev Biomed Eng. 2002;4:129-53
pubmed: 12117754
Sci Data. 2018 Sep 04;5:180176
pubmed: 30179232
Science. 2014 Nov 28;346(6213):1258096
pubmed: 25430774
Nucleic Acids Res. 2015 Jan;43(Database issue):D935-9
pubmed: 25300487
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Genome Biol Evol. 2015 May 28;7(6):1761-78
pubmed: 26025559
F1000Res. 2018 Jul 24;7:
pubmed: 30079234
Trends Microbiol. 2018 Nov;26(11):955-965
pubmed: 29937307
Nucleic Acids Res. 2012 Jan;40(Database issue):D57-63
pubmed: 22139929
Metabolomics. 2009 Dec;5(4):435-458
pubmed: 20046865
Genome Biol Evol. 2019 Jan 1;11(1):109-120
pubmed: 30496396
Database (Oxford). 2017 Jan 1;2017:
pubmed: 29220460
Mar Drugs. 2019 Jun 01;17(6):
pubmed: 31159359
Nat Biotechnol. 2010 Jul;28(7):710-21
pubmed: 20622845
J Nat Prod. 2012 Oct 26;75(10):1833-77
pubmed: 23009278
Nat Prod Rep. 2019 Oct 16;36(10):1412-1436
pubmed: 30620035
Curr Opin Chem Biol. 2017 Feb;36:15-23
pubmed: 28064089
BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):443
pubmed: 30497362
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Mar Drugs. 2019 Mar 26;17(3):
pubmed: 30917600
Mar Drugs. 2017 May 18;15(5):
pubmed: 28524092
Front Microbiol. 2019 Mar 21;10:552
pubmed: 30949149
Front Microbiol. 2018 Aug 21;9:1910
pubmed: 30186253
Nutrients. 2019 May 29;11(6):
pubmed: 31146462
Mar Drugs. 2018 Dec 07;16(12):
pubmed: 30544522
J Sci Food Agric. 2019 Jan 15;99(1):13-24
pubmed: 29797494
PLoS One. 2015 Apr 24;10(4):e0124633
pubmed: 25909470
Appl Environ Microbiol. 2012 Jan;78(2):589-92
pubmed: 22057866
Sci Data. 2019 Jun 20;6(1):97
pubmed: 31222011
FEMS Microbiol Rev. 2011 Nov;35(6):993-1034
pubmed: 21204862
Nucleic Acids Res. 2018 Jan 4;46(D1):D624-D632
pubmed: 29145643
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Mol Recognit. 1996 Jan-Feb;9(1):1-5
pubmed: 8723313
Nature. 2001 Jun 14;411(6839):786-9
pubmed: 11459054
Hum Genomics Proteomics. 2009 Dec 08;2009:
pubmed: 20948568
PLoS Biol. 2011 Aug;9(8):e1001127
pubmed: 21886479
Nature. 2016 Aug 11;536(7615):179-83
pubmed: 27487207
Mar Drugs. 2018 Nov 21;16(11):
pubmed: 30469402
New Microbes New Infect. 2014 Nov;2(6):161-9
pubmed: 25566394
Sci Rep. 2017 Mar 06;7:43417
pubmed: 28262802
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87
pubmed: 31032519
Curr Opin Chem Biol. 2008 Oct;12(5):483-90
pubmed: 18718552
Biochemistry. 2018 Dec 4;57(48):6715-6725
pubmed: 30418016
Nucleic Acids Res. 2018 Jan 4;46(D1):D8-D13
pubmed: 29140470
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101
pubmed: 29771380
J Proteomics. 2014 Jun 13;105:92-106
pubmed: 24788067
Sci Adv. 2018 Jun 06;4(6):eaar5237
pubmed: 29881777
Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5
pubmed: 24270786