BAC is the acronym for "bacterial artificial chromosome. The fragments are cloned in bacteria, which store and replicate the human DNA so that it can be prepared in quantities large enough for sequencing.
If carefully chosen to minimize overlap, it takes about 20, different BAC clones to contain the 3 billion pairs of bases of the human genome. Using this approach ensures that scientists know both the precise location of the DNA letters that are sequenced from each clone and their spatial relation to sequenced human DNA in other BAC clones.
For sequencing, each BAC clone is cut into still smaller fragments that are about 2, bases in length. These pieces are called "subclones.
The products of the sequencing reaction are then loaded into the sequencing machine sequencer. The sequencer generates about to base pairs of A, T, C and G from each sequencing reaction, so that each base is sequenced about 10 times. A computer then assembles these short sequences into contiguous stretches of sequence representing the human DNA in the BAC clone.
This was intentionally not known to protect the volunteers who provided DNA samples for sequencing. The sequence is derived from the DNA of several volunteers. To ensure that the identities of the volunteers cannot be revealed, a careful process was developed to recruit the volunteers and to collect and maintain the blood samples that were the source of the DNA. The volunteers responded to local public advertisements near the laboratories where the DNA "libraries" were prepared.
Candidates were recruited from a diverse population. The volunteers provided blood samples after being extensively counseled and then giving their informed consent. About 5 to 10 times as many volunteers donated blood as were eventually used, so that not even the volunteers would know whether their sample was used.
All labels were removed before the actual samples were chosen. The main goals of the Human Genome Project were first articulated in by a special committee of the U. National Academy of Sciences, and later adopted through a detailed series of five-year plans jointly written by the National Institutes of Health and the Department of Energy.
The principal goals laid out by the National Academy of Sciences were achieved, including the essential completion of a high-quality version of the human sequence. Other goals included the creation of physical and genetic maps of the human genome, which were accomplished in the mids, as well as the mapping and sequencing of a set of five model organisms, including the mouse.
All of these goals were achieved within the time frame and budget first estimated by the NAS committee. Notably, quite a number of additional goals not considered possible in have been added along the way and successfully achieved.
Examples include advanced drafts of the sequences of the mouse and rat genomes, as well as a catalog of variable bases in the human genome. On June 26, , the International Human Genome Sequencing Consortium announced the production of a rough draft of the human genome sequence.
In April, , the International Human Genome Sequencing Consortium is announcing an essentially finished version of the human genome sequence. This version, which is available to the public, provides nearly all the information needed to do research using the whole genome. The difference between the draft and finished versions is defined by coverage, the number of gaps and the error rate. There are two sequencing read types: single-read and paired-end sequencing.
Single-read sequencing involves sequencing DNA fragments from one end to the other. It is useful for some applications, such as small RNA sequencing, and can be a fast and economical option. With paired-end sequencing, after a DNA fragment is read from one end, the process starts again in the other direction. In addition to producing twice the number of sequencing reads, this method enables more accurate read alignment and detection of structural rearrangements.
Today, most researchers use the paired-end approach. This tool provides recommended read lengths for different methods and Illumina library prep kits. All Illumina sequencing reagents feature a certain number of sequencing cycles. These cycles are directly related to sequencing read length. Because one base is sequenced per cycle, the total number of cycles indicates the maximum number of bases that can be sequenced.
You can use sequencing reagents to generate single continuous reads or for paired-end sequencing in both directions. Considering bringing next-generation sequencing to your lab, but unsure where to start?
These resources cover key topics in NGS and are designed to help you plan your first experiment. The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution.
Mol Biol Evol. First exons and introns—a survey of GC content and gene structure in the human genome. Identification and validation of evolutionarily conserved unusually short Pre-mRNA introns in the human genome. Int J Mol Sci. DNA Res. TRAM Transcriptome Mapper : database-driven creation and analysis of transcriptome maps from multiple sources. BMC Genomics. A quantitative transcriptome reference map of the normal human brain. BMC Med Genomics. A quantitative transcriptome reference map of the normal human hippocampus.
Integrated transcriptome map highlights structural and functional aspects of the normal human Heart. J Cell Physiol. Universal tight correlation of codon bias and pool of RNA codons codonome : The genome is optimized to allow any distribution of gene expression values in the transcriptome from bacteria to humans. Mamm Genome. An estimation of the number of cells in the human body.
Ann Hum Biol. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity. Genome structural variation discovery and genotyping. Nat Rev Genet. An integrated map of structural variation in human genomes. A global reference for human genetic variation. Bonnici V, Manca V. Informational laws of genome structures.
Sci Rep. Co-expression of fibulin-5 and VEGF increases long-term patency of synthetic vascular grafts seeded with autologous endothelial cells. Gene Ther. Plasma and urinary metabolomic profiles of Down Syndrome correlate with alteration of mitochondrial metabolism. Integrated quantitative transcriptome maps of human trisomy 21 tissues and cells. Front Genet. Systematic reanalysis of partial trisomy 21 cases with or without Down Syndrome suggests a small region on 21q Hum Mol Genet.
Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics. BMC Bioinformatics. GeneBase 1. Database Oxford. Bogenhagen DF. Mitochondrial DNA nucleoid structure. Biochim Biophys Acta. Structural and compositional features of untranslated regions of eukaryotic mRNAs. Int J Mol Med. Molecular structure of a double helical DNA fragment intercalator complex between deoxy CpG and a terpyridine platinum compound.
Download references. AP developed the software, collected the data, performed the analysis, and wrote the manuscript draft. MCP and FA collected the data and critically revised the results of the analysis. PS designed the work, tested the software and wrote the manuscript draft.
MC and LV supervised the project and critically revised the manuscript. All authors contributed to the interpretation of data. All authors read and approved the final manuscript.
We wish to sincerely thank the Fondazione Umano Progresso, Milano, Italy for their fundamental support to our research on trisomy 21 and to this study. We thank all the other people that very kindly contributed by individual donations to support part of the fellowships as well as hardware and software. Some of them are also are available within the article and its additional information files.
Minimum software requirements: Mac OS X Minimum system requirements: Mac OS X A connection to the Internet is required to display the software tutorial and to download data for set up, but not to run the tool. This work was supported by donations from Fondazione Umano Progresso and from other donors acknowledged below which supported the purchase of the hardware and software that were necessary to conduct the research. The funding sources had no role in the design of this study and collection, analysis, and interpretation of data and in writing the manuscript.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. You can also search for this author in PubMed Google Scholar. Correspondence to Maria Caracausi. Human genome length and weight calculations, human GC content analysis and GC content analysis in other species. Detailed description of the genome length and weight calculations and of the GC content analysis for the human genome and for Danio rerio , Caenorhabditis elegans , Saccharomyces cerevisiae , and Escherichia coli.
Nucleotide counts in the 24 human chromosomes and estimation of uncertain bases, based on GRCh Nucleotide counts for the 24 human chromosomes and estimation of uncertain bases necessary for the genome length and weight calculations and for the GC content analysis, based on the most recent human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file. Nucleotide counts for the 24 human chromosomes and estimation of uncertain bases necessary for the genome length and weight calculations and for the GC content analysis, based on the previous human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file.
Length, weight and GC content of human chromosomes, genome and mitochondrial DNA, based on the previous human genome assembly, obtained as described in detail in Additional file 1 : Additional Methods file. Accordance of our calculations with previous reports.
Accordance with previous reports of our calculations of the number of chromosomes and the total genome length for Danio rerio , Caenorhabditis elegans , Saccharomyces cerevisiae , and Escherichia coli obtained as described in detail in Additional file 1 : Additional Methods file.
Reprints and Permissions. Piovesan, A. On the length, weight and GC content of the human genome. BMC Res Notes 12, Download citation.
0コメント