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PMC:PMC3636130 JSONTXT

Divisions (24) JSON TSV

div. section text # proj. length # Ann.
0 TIAB The Genome Organization ofThermotoga maritimaReflects Its Lifestyle The generation of genome-scale d 1 1936 0 show
1 Introduction A fundamental step towards obtaining a systems-level understanding of organisms is to obtain an accu 1 6020 0 show
2 Results An integrative, multi-omic approach for the annotation of the genome organization An integrative wor 1 6498 0 show
3 Results Identification of promoters and RBSs followed by quantitative intra- and interspecies analysis of bi 1 9481 0 show
4 Results T. maritima promoter-containing intergenic regions reveal a unique distribution of 5′UTRs and spatia 1 3757 0 show
5 Results T. maritima has an actively transcribed genome that is tightly correlated to protein abundances Tran 1 870 0 show
6 Discussion Genome-scale technologies have provided researchers unprecedented access to large volumes of data de 1 7049 0 show
7 Materials and Methods Culture conditions and physiology T. maritima MSB8 ATCC derived cultures were grown at 80°C under an 1 1573 0 show
8 Materials and Methods Genome resequencing and annotation updates The recent identification of a 9 kb gap in the T. maritim 1 1455 0 show
9 Materials and Methods Transcription start site determination Total RNA was isolated from log phase cultures using the hot 1 665 0 show
10 Materials and Methods Transcriptome characterization and gene expression Tiling array and RNA-seq data were generated unde 1 1570 0 show
11 Materials and Methods Proteomics, peptide mapping, and protein abundance quantitation Proteomics samples and data were gen 1 2484 0 show
12 Materials and Methods Promoter element motif analysis and position weight matrix (PWM) generation The process of determini 1 1575 0 show
13 Materials and Methods Information content calculations Position weight matrices (PWMs) for each promoter element were conv 1 2138 0 show
14 Materials and Methods Ribosome binding site energy calculations The anti-RBS sequence 5′-UCACCUCCUU-3′ (3′ end of the 16S 1 1955 0 show
15 Materials and Methods Rho-independent terminator site determination Intrinsic terminators were predicted using the TransTe 1 340 0 show
16 Materials and Methods Prediction of small RNAs Small RNAs were predicted with Infernal [39] using cmsearch with default se 1 376 0 show
17 Materials and Methods Transcription unit assembly TU assembly was accomplished through an iterative procedure beginning wi 1 1217 0 show
18 Materials and Methods Transcription factor binding site mapping TF binding sites were extracted from RegPrecise [57] and c 1 198 0 show
19 Materials and Methods Data deposition The T. maritima MSB8 ATCC (genomovar) genome and annotation are found under Genbank 1 321 0 show
20 Caption-Figure 1 Generation of multiple genome-scale datasets integrated with bioinformatics predictions reveals the 1 840 0 show
21 Caption-Figure 2 Identification and quantitative comparison of genetic elements for transcription and translation ini 1 2979 0 show
22 Caption-Figure 3 Arrangement of genomic features contained within promoter-containing intergenic regions (PIRs). (A) 1 756 0 show
23 Caption-Figure 4 Global analysis of mRNA and protein expression levels. (A) The fraction of transcribed genes as a fu 1 910 0 show