Draft genome sequence of the Lactobacillus agilis strain Marseille

Genome Announcements

Volumn 3, Issue 4, 2015, Pages

  Drissi, Fatima ^a   Labas, Noémie ^a   Merhej, Vicky ^a   Raoult, Didier ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85008506923     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00840-15     Document Type: Article

References (14)

1. Spoelstra MN, Mari A, Mendel M, Senga E, van Rheenen P, van Dijk TH, Reijngoud DJ, Zegers RG, Heikens GT, Bandsma RH. 2012. Kwashiorkor and marasmus are both associated with impaired glucose clearance related to pancreatic β-cell dysfunction. Metabolism 61:1224-1230. http://dx.doi.org/10.1016/j.metabol.2012.01.019.
2. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI. 2013 Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339:548-554. http://dx.doi.org/10.1126/science.1229000.
3. Rohr LM, Teuber M, Meile L. 2002. Phosphoketolase, a neglected enzyme of microbial carbohydrate metabolism. Chimia Int J Chem 56: 270-273.
4. Zerbino DR. 2010. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics Chapter 11:Unit 11.5. http://dx.doi.org/10.1002/0471250953.bi1105s31.
5. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578-579. http://dx.doi.org/10.1093/bioinformatics/btq683.
6. Gao S, Sung WK, Nagarajan N. 2011. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 18:1681-1691. http://dx.doi.org/10.1089/cmb.2011.0170.
7. Boetzer M, PirovanoW. 2012. Toward almost closed genomes with Gap-Filler. Genome Biol 13:R56. http://dx.doi.org/10.1186/gb-2012-13-6-r56.
8. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100-3108. http://dx.doi.org/10.1093/nar/gkm160.
9. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11-16. http://dx.doi.org/10.1093/nar/gkh152.
10. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: an RNA family database. Nucleic Acids Res 31:439-441. http://dx.doi.org/10.1093/nar/gkg006.
11. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Res 40:D290-D301. http://dx.doi.org/10.1093/nar/gkr1065.
12. Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25:1335-1337. http://dx.doi.org/10.1093/bioinformatics/btp157.
13. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010 Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119.
14. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421. http://dx.doi.org/10.1186/1471-2105-10-421.