{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:30:19Z","timestamp":1761611419572,"version":"3.37.3"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["281384\u2013FuMe"],"award-info":[{"award-number":["281384\u2013FuMe"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1668-y","type":"journal-article","created":{"date-parts":[[2017,5,22]],"date-time":"2017-05-22T13:20:24Z","timestamp":1495459224000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["In silico approach to designing rational metagenomic libraries for functional studies"],"prefix":"10.1186","volume":"18","author":[{"given":"Anna","family":"Kusnezowa","sequence":"first","affiliation":[]},{"given":"Lars I.","family":"Leichert","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,5,22]]},"reference":[{"key":"1668_CR1","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1371\/journal.pbio.0050016","volume":"5","author":"S Yooseph","year":"2007","unstructured":"Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, et al. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 2007;5:432\u201366.","journal-title":"PLoS Biol"},{"issue":"5","key":"1668_CR2","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/nbt0507-540","volume":"25","author":"EV Koonin","year":"2007","unstructured":"Koonin EV. Metagenomic sorcery and the expanding protein universe. Nat Biotechnol. 2007;25(5):540\u20132.","journal-title":"Nat Biotechnol"},{"key":"1668_CR3","doi-asserted-by":"crossref","first-page":"D213","DOI":"10.1093\/nar\/gku1243","volume":"43","author":"A Mitchell","year":"2015","unstructured":"Mitchell A, Chang H-Y, Daugherty L, Fraser M, Hunter S, Lopez R, et al. The InterPro protein families database: the classification resource after 15\u00a0years. Nucleic Acids Res. 2015;43:D213\u201321.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR4","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/ismej.2011.2","volume":"5","author":"I Sharon","year":"2011","unstructured":"Sharon I, Battchikova N, Aro E-M, Giglione C, Meinnel T, Glaser F, et al. Comparative metagenomics of microbial traits within oceanic viral communities. ISME J. 2011;5:1178\u201390.","journal-title":"ISME J"},{"key":"1668_CR5","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nmeth.2340","volume":"10","author":"P Radivojac","year":"2013","unstructured":"Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, et al. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013;10:221\u20137.","journal-title":"Nat Methods"},{"key":"1668_CR6","doi-asserted-by":"crossref","first-page":"D290","DOI":"10.1093\/nar\/gkr1065","volume":"40","author":"M Punta","year":"2012","unstructured":"Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290\u2013301.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR7","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/nar\/gkg128","volume":"31","author":"DH Haft","year":"2003","unstructured":"Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371\u20133.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR8","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195\u20135.","journal-title":"PLoS Comput Biol"},{"key":"1668_CR9","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/978-1-61779-361-5_15","volume":"804","author":"S Van Dongen","year":"2012","unstructured":"Van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol. 2012;804:281\u201395.","journal-title":"Methods Mol Biol"},{"key":"1668_CR10","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K-I, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059\u201366.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR11","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1186\/1471-2105-8-312","volume":"8","author":"R Gouveia-Oliveira","year":"2007","unstructured":"Gouveia-Oliveira R, Sackett PW, Pedersen AG. MaxAlign: maximizing usable data in an alignment. BMC Bioinformatics. 2007;8:312.","journal-title":"BMC Bioinformatics"},{"key":"1668_CR12","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.","journal-title":"BMC Bioinformatics"},{"key":"1668_CR13","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","volume":"56","author":"G Talavera","year":"2007","unstructured":"Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564\u201377.","journal-title":"Syst Biol"},{"key":"1668_CR14","volume":"7","author":"M Wu","year":"2012","unstructured":"Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLoS One. 2012;7, e30288.","journal-title":"PLoS One"},{"key":"1668_CR15","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btt357","volume":"29","author":"Y Zhang","year":"2013","unstructured":"Zhang Y, Sun Y, Cole JR. A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads. Bioinformatics. 2013;29:2103\u201311.","journal-title":"Bioinformatics"},{"key":"1668_CR16","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gkt1274","volume":"42","author":"T Tatusova","year":"2014","unstructured":"Tatusova T, Ciufo S, Fedorov B, O\u2019Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42:D553\u20139.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR17","doi-asserted-by":"crossref","first-page":"D571","DOI":"10.1093\/nar\/gku1207","volume":"43","author":"JR Brister","year":"2015","unstructured":"Brister JR, Ako-Adjei D, Bao Y, Blinkova O. NCBI viral genomes resource. Nucleic Acids Res. 2015;43:D571\u20137.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR18","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/S0958-1669(02)00341-5","volume":"13","author":"K-E Jaeger","year":"2002","unstructured":"Jaeger K-E, Eggert T. Lipases for biotechnology. Curr Opin Biotechnol. 2002;13:390\u20137.","journal-title":"Curr Opin Biotechnol"},{"key":"1668_CR19","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","volume":"22","author":"W Li","year":"2006","unstructured":"Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658\u20139.","journal-title":"Bioinformatics"},{"key":"1668_CR20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001638","volume":"11","author":"BP Anton","year":"2013","unstructured":"Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, Guleria J, et al. The COMBREX project: design, methodology, and initial results. PLoS Biol. 2013;11, e1001638.","journal-title":"PLoS Biol"},{"key":"1668_CR21","doi-asserted-by":"crossref","first-page":"e0131624","DOI":"10.1371\/journal.pone.0131624","volume":"10","author":"K Daiha","year":"2015","unstructured":"Daiha K, De G, Angeli R, De Oliveira SD, Almeida RV. Are Lipases Still Important Biocatalysts? A Study of Scientific Publications and Patents for Technological Forecasting. PLoS One. 2015;10:e0131624.","journal-title":"PLoS One"},{"key":"1668_CR22","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gki376","volume":"33","author":"A Grote","year":"2005","unstructured":"Grote A, Hiller K, Scheer M, M\u00fcnch R, N\u00f6rtemann B, Hempel DC, et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33:W526\u201331.","journal-title":"Nucleic Acids Res"},{"key":"1668_CR23","volume-title":"Molecular Cloning","author":"J Sambrook","year":"2001","unstructured":"Sambrook J, Russell DW. Molecular Cloning. New York: Cold Spring Habor; 2001."},{"key":"1668_CR24","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1128\/JB.62.3.293-300.1951","volume":"62","author":"G Bertani","year":"1951","unstructured":"Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951;62:293\u2013300.","journal-title":"J Bacteriol"},{"key":"1668_CR25","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1128\/AEM.53.1.211-213.1987","volume":"53","author":"G Kouker","year":"1987","unstructured":"Kouker G, Jaeger KE. Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol. 1987;53:211\u20133.","journal-title":"Appl Environ Microbiol"},{"key":"1668_CR26","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.3389\/fmicb.2015.01110","volume":"6","author":"T Masuch","year":"2015","unstructured":"Masuch T, Kusnezowa A, Nilewski S, Bautista JT, Kourist R, Leichert LI. A combined bioinformatics and functional metagenomics approach to discovering lipolytic biocatalysts. Front Microbiol. 2015;6:1110.","journal-title":"Front Microbiol"},{"key":"1668_CR27","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","volume":"43","author":"UniProt Consortium","year":"2015","unstructured":"UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204\u201312.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1668-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,8]],"date-time":"2020-10-08T06:08:37Z","timestamp":1602137317000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1668-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,22]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1668"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1668-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2017,5,22]]},"article-number":"267"}}