Take-Home Message comic #5 celebrates an amazing milestone. During my PhD, I kept a little list pinned to the filing cabinet next to my desk, a list which contained details of every sequenced genome. This was something that was much easier when the number of published genomes was still in the single digits!. This is my favorite Take-Home Message comic to date. I feel that we are slowly settling in on a style that works well for this medium, and Abbys drawings just seem to get better and better. ...
TY - JOUR. T1 - Draft genome sequences of Escherichia coli strains isolated from septic patients. AU - Dunitz, Madison I.. AU - Coil, David A.. AU - Jospin, Guillaume. AU - Eisen, Jonathan A. AU - Adams, Jason Yeates. PY - 2014. Y1 - 2014. N2 - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. AB - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. UR - ...
It has been suggested that environmental constraints strongly shape nucleotide composition [26, 49-51]. If this were the case, two effects should be apparent in genome signatures of AMD populations. First, shared pressures deriving from the extreme AMD environment would drive genome signatures together, potentially obscuring differences between populations. Second, since each genome encodes proteins destined for diverse environments (that is, intracellular and extracellular), there should be prominent intra-genome variation of genome signature and scattering of fragments from the same genome into disparate regions of the SOM. Neither of these expectations is met in the AMD dataset. There are vast differences in nucleotide composition between populations, with genomic %GC ranging from 35% (ARMAN-4 and ARMAN-5) to 69% (low-abundance Actinobacteria) and genome signatures forming discrete clusters. Amino acid compositional constraints required for stability of proteins exposed to acidic solutions do ...
One realization that has come from comparing multiple bacterial genome sequences, including multiple isolates from the same species, is that gene transfer is an important force in bacterial genome evolution. In the laboratory gene transfer is essential for the study of bacteria and for learning more about all living organisms. Three processes in bacteria can broadly define the transfer of DNA: transformation, transduction, and conjugation. This chapter focuses on the many genetic tools available to manipulate the genetic content of Escherichia coli. A DNA molecule that does not have its own origin of replication must integrate into either the host chromosome or another autonomously replicating element such as an endogenous plasmid. In E. coli a modified derivative of the bacteriophage T4 offers some advantages for transduction in that it packages twice as much DNA as P1 and also is less sensitive to capsules found on many pathogenic strains of E. coli. Transformation of bacteria by use of either
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of ...
Functional annotation of genomes is a critical aspect of the genomics enterprise. Without reliable assignment of gene function at the appropriate level of specificity, new genome sequences are plainly useless. The primary methodology used for genome annotation is the sequence database search, the results of which allow transfer of functional information from experimentally characterized genes (proteins) to their uncharacterized homologs in newly sequenced genomes [1,2,3]. However, general-purpose, archival sequence databases are not particularly suited for the purpose of genome annotation. The quality of the annotation of a new genome produced using a particular database critically depends on the reliability and completeness of the annotations in the database itself. As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached to each sequence by its submitter. In their capacity as sequence archives, such databases include no ...
BacMap is a freely available web-accessible database containing fully annotated, fully zoomable and fully searchable chromosome maps from more than 2500 prokaryotic (archaebacterial and eubacterial) species.[1] BacMap was originally developed in 2005 to address the challenges of viewing and navigating through the growing numbers of bacterial genomes that were being generated through large-scale sequencing efforts. Since it was first introduced, the number of bacterial genomes in BacMap has grown by more than 15X. Essentially BacMap functions as an on-line visual atlas of microbial genomes. All of the genome annotations in BacMap were generated through the BASys genome annotation system.[3] BASys is a widely used microbial annotation infrastructure that performs comprehensive bionformatic analyses on raw (or labeled) bacterial genome sequence data. All of the genome (chromosome) maps in BacMap were constructed using the program known as CGView.[4] CGView is a popular visualization program for ...
Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count. ...
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.
In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[7] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of ...
sec id="bid.36", ,title,Microbial Genomes,/title, ,p,... A CON entry, containing instructions on how to put the pieces back together, is also made. The CON entry contains descriptor information, such as source organism and references, as well as a join statement providing explicit instructions on how to generate the complete genome from the pieces. The Accession number assigned to the CON record is also added as a secondary Accession number on each of the pieces that make up the complete genome (see ,xref ref-type="fig" rid="bid.37",Figure 2,/xref,). ,fig id="bid.37", ,label,2,/label, ,caption,,title,A GenBank CON entry for a complete bacterial genome.,/title, ,p,The information toward the ,italic,bottom,/italic, of the record describes how to generate the complete genome from the pieces.,/p, ,/caption, ,graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ch1f2" mime-subtype="gif"/, ,/fig, ,/p, ... ,/sec ...
In 1995, the release of the first fully sequenced bacterial genome heralded a new era of bacterial genomic research (21). Over the past 20 years, the number of sequenced bacterial genomes has risen exponentially, and new research strategies, techniques, and applications have emerged to exploit the opportunities that these resources provide. While raw genomic sequence data are valuable, the availability of fully annotated genome sequences, outlining the positions of known genes and genomic features, dramatically increases their utility. Global expression analysis techniques such as microarrays and RNA-seq depend heavily on annotated genome sequences as a reference source for genes in the bacterial cell. These techniques have proved extremely useful; however, recently, certain limitations to their application are becoming apparent. A major concern in this regard is that they do not provide expression data for genes that are not included in genome annotation files. Bacterial sRNAs represent a class ...
Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the
Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former soft core of about 3,000 gene families is perhaps more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST
Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of paramount importance. However, increasing evidence indicates that currently annotated bacterial genomes have missed many genes encoding small proteins ≤60 aa (Wood et al. 2012; Warren et al. 2010). A small gene, or a small open reading frame (sORF), has previously been defined as one encoding proteins of ≤60 aa (Hemm et al. 2010); or alternatively, it accommodates those up to 100 aa (Andrews and Rothnagel 2014). While small proteins have been increasingly reported for their important cellular roles in bacteria (Alix and Blanc-Potard 2008; Martin et al. 2015; Hobbs et al. 2012), studies on small proteins are limited, partly because many small genes are unannotated in sequenced bacterial genomes (Alix and Blanc-Potard 2009; Storz et al. 2014). Despite much effort made to improve gene annotation, the accurate identification of small genes has been a persistent challenge ...
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Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of E. coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive
Given the size of modern sequence databases, finding the complete genome sequence for a bacterium among the many other partial sequences can be a challenge. In addition, if you want to download sequences for many bacterial species, an automated solution might be preferable. In this post well discuss how to download bacterial genomes programmatically for…
A potential user (customer) of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to write this post. The suggestions below are not absolute, just my thoughts on how one these days could go about sequencing a bacterial genome using one or more of the sequencing…
The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and Gram(+) bacteria. This kit combines the advantages of a silica-based system with a microspin format, eliminating the need for expensive resins and hazardous organic compounds.
The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. ...
Species identification by sequencing the bacterial genome at seven key loci, uncovering achieved similar combinations of sequences with certain bacterial
Harvard scientists have unraveled the inner architecture of bacterial genomes in a breakthrough discovery that may shed light on how chromosomes organize within a cell.. The findings came after researchers applied a new visualization technique that generated the first fluorescence super-resolution images of chromosomes within a single bacterial cell.. The work demonstrates "the massive potential provided by the combination of emerging super-resolution microscopy and clever biochemistry," wrote Stefan W. Hell, director at the Max Planck Institute for Biophysical Chemistry, in an emailed statement. He added that the findings "open a new chapter in the study of bacteria molecular organization.". The findings provide the first detailed picture of a class of DNA-interacting proteins called nucleoid-associated proteins (NAPs). This close-up look helped scientists determine their role in organizing chromosomes in bacteria, according to Xiaoliang Sunney Xie, a Harvard professor of chemistry and chemical ...
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe
Scientists at Harvard have used a modified CRISPR gene editing tool to insert coded sequences into bacterial genomes matching a video clip.
Pan-Genomic Approaches for Comprehensive Screening of Novel or Emerging Infectious Agents in Blood Emerging infectious agents, the latest of which is Zika virus...
The workshop will focus on the design and analysis of pan-genomic microarrays. Due to the massive availability of sequences of genomes of microbes and other organisms, the degree of sequence variation is becomming measurable both across bacterial species, but also within different isolates of the same species. Indeed, the pan-genome, defined as the total number of unique genes observed in any isolates of a given species, can be much larger than the individual genome of any single isolate. For the microarray analyst, genetic variation between isolates of the same species presents new challenges since a traditional microarray designed to target one specific genome is likely to perform very poorly if used with another, different isolate. As the number of fully sequenced genomes of indepentent isolates for each bacterial species increases, it becommes possible to design pan-genomic microarrays capable of targeting any and all unique genes ever observed in that species. The advantages of this ...
The first step of bacterial cloning is to get the gene of interest into the bacterial genome. Bacteria are one-celled, prokaryotic organisms and have simpler cellular structures than humans, who are complex and multi-cellular eukaryotes. The genomes of each are stored slightly differently: both rely on large, long structures of DNA called chromosomes, but while you can think of a bacterial genome as one large, single circle of DNA twisted up like a convoluted rubber band and free-floating in the bacterial cell, the human chromosome structure (26 chromosomes in total) is a long linear string of DNA twisted up and tucked away neatly into a sub-packet of the cell called the nucleus-think what happens to your headphones when you put them in your pocket. In addition to their larger, circular chromosome, bacteria have other small, circular, free-floating pieces of DNA called plasmids. These plasmids are maintained and copied separately from the larger circular chromosome. Because bacteria can pick up ...
Eric Smalley writes The worlds largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with graphics chips — the sort of processors that were originally designed to draw images on your personal ...
Multiplex automated genome engineering (MAGE) is a powerful technology for in vivo genome editing that uses synthetic single-stranded DNA (ssDNA) to introduce targeted modifications directly into the Escherichia coli chromosome. MAGE is a cyclical process that involves transformation of ssDNA (by el …
MAGE, the older of the two techniques, made its debut two years ago. It stands for "multiplex automated genome engineering", a fancy way of saying that it can easily change a genome many times over. It was originally used to create millions of small variants of bacterial genomes, producing a multitude of strains that can be tested for new abilities. As Jo Marchant puts it in her excellent feature, its an "evolution machine". In its debut, within a matter of days, it had evolved a strain of E.coli that would produce large amounts of lycopene, a pigment that makes tomatoes red.. MAGE is a versatile editor. Not only can it create many diverse changes in a group of cells, it can also create many specific changes in a single cell. Thats what Isaacs, Carr and Wang have now done. TAG appears in 314 places throughout the E.coli genome as a stop codon. For each one, the team created a small stretch of DNA that had TAA instead of TAG, surrounded by exactly the same letters. They fed these edited ...
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome ...
Bacteria generate small molecules to fend off their fellow microbes. They also produce molecules that affect the response of host organisms-including humans-to their presence. Such molecules have been a major source of antibiotics, immunosuppressants, anti-cancer agents, and other drugs. But their discovery has not been systematic and the products of bacteria living in our bodies have only recently drawn scientific notice.. However, thanks to genome sequencing, there are now databases containing the blueprints (sequences) of 160 million genes from nearly a quarter-million organisms, including the genes of bacteria species that live in and interact with us-the human microbiome. These bacterial genes encode molecules that could yield narrow-spectrum antibiotics, immune system regulators, and neuroactive drugs. But first scientists must find the potentially therapeutic needles in this genomic haystack.. Research in the laboratory of Michael Fischbach, PhD, a faculty member of the UCSF School of ...
We can think of the bacterial genome as having two parts," says Professor Young. "The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world ...
Use bioinformatics to explore DNA sequences and protein functions, to find the determinants of virulence in microbes with this free online course.
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL., Nature 430(6995), 2004 ...
Back to the clever bit, the authors realized that putting these plasmids into E.coli represents HGT. These vectors are in fact derived from natural E.coli strains and are transferred naturally between strains. So, through the process of obtaining genome sequence for a variety of bacterial species, Sorek et al realized that the scientific community had inadvertantly set up an experiment to determine the limits of HGT. They simply (and by "simply" I mean anyone with a computer and knowledge of these systems could have done it, it is not meant to diminish the work or insights of the authors) took available genome sequence information from 79 distinct species and looked to see what was not sequenced using the process described above. Again, the idea being if a region was not sequenced, it must not have been propagated in E.coli (the gaps in a genome sequence are obtained using other more labor intensive methods). Indeed, the authors found regions from these species that were not able to be ...
Scientists at the J. Craig Venter Institute (JCVI), a genomics research facility, transplanted a bacterial chromosome from one type of bacteria into anothe
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The Neolithic revolution, and the corresponding transition to agricultural and pastoralist lifestyles, represents one of the greatest cultural shifts in human history, and it has long been hypothesized that this might have ...
Scientific American is the essential guide to the most awe-inspiring advances in science and technology, explaining how they change our understanding of the world and shape our lives.
TCGA tumor genome sequencing analyses offer new insights into the effects of HPV and smoking, and find genomic similarities with other cancers.
New genome sequence highlights corns adaptability,University of Hawaiʻi at Mānoa researchers contributed to an historic release of a new, high-quality
ATCC provides all the cultures you need to perform complex analysis of sequenced genomes, including fungi, yeasts, bacteria, and protozoa.
ATCC provides all the cultures you need to perform complex analysis of sequenced genomes, including fungi, yeasts, bacteria, and protozoa.
Whole genome sequencing has become an essential tool for researchers. But slow speeds and high costs have helped keep the technology from becoming a
Students in the Gene and Genome Analysis class (taught by Dr. Elsbeth Walker) characterize the activity of a novel gene in Arabidopsis.. ...
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Study of the mechanisms by which imported pieces of DNA find their integration sites on host bacterial genomes in live individual bacteria.. ...
To what extent is it possible to predict the phenotypic differences amongst individuals from their completely sequenced genomes? We use model organisms (yeast, worms) and computational analyses to understand when you can, and why you cannot, predict the biology of an individual from their genome sequence. Individuals are thankfully all different, and our aim is to understand how these differences originate in the interactions between genetic, environmental, life history, parental and stochastic sources of variation.. ...
I ordered the 23andme kit. I was originally going to get my full genome sequenced, but I cant afford that at this time. I was then going to wait, but the situation is urgent enough that I need to do something now. So, Im going with the 23andme kit until Im working again (and making money) and am able to afford something more comprehensive. I know many SNPs dont have any research associated with them, but the idea is to get the entire thing done once, such that I can continually refer back
I ordered the 23andme kit. I was originally going to get my full genome sequenced, but I cant afford that at this time. I was then going to wait, but the situation is urgent enough that I need to do something now. So, Im going with the 23andme kit until Im working again (and making money) and am able to afford something more comprehensive. I know many SNPs dont have any research associated with them, but the idea is to get the entire thing done once, such that I can continually refer back
Of the 21 bacterial genomes that have so far been sequenced in their entirety, 16 are from pathogenic species. One of the main attractions to the complete sequencing of microbial genomes has been the potential to understand more readily the molecular biology of these important pathogens, and thereby obtain crucial insights that would lead to the development of vaccines and antimicrobials. The move from the relatively simple annotation of genes in a genome to insights into their function, however, is not a trivial task. Diverse approaches to exploit the utility and influence of microbial genome sequences on whole organism biology were highlighted in this session; each speaker tackled the issue of how best to take advantage of the available genome sequence information in a different way.. The Neisseria meningitidis serogroup B strain MC58 sequence has been used to identify novel vaccine candidates that are now being actively pursued (Rino Rappouli, Chiron SpA). Using the recently completed ...
Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive alignment techniques. These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences. We present a new method of multiple sequence alignment, called MISHIMA (Method for Inferring Sequence History In terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm is used to quickly find rare oligonucleotide sequences shared by all sequences. Divide and conquer approach is then applied to break the sequences into fragments that can be aligned independently by an external alignment program. These partial alignments are assembled together to form a complete alignment of the original sequences.
In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster
Obradović, Davor, et al. "A Cytolethal Distending Toxin Variant from Aggregatibacter actinomycetemcomitans with an Aberrant CdtB That Lacks the Conserved Catalytic Histidine 160." PloS one 11.7 (2016): e0159231.. Hemp, James, et al. "Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae." Genome Announcements 3.6 (2015): e01353-15.. Ward, Lewis M., et al. "Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae." Genome Announcements 3.6 (2015): e01356-15.. Hemp, James, et al. "Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae." Genome Announcements 3.6 (2015): e01357-15.. Hemp, James, et al. "Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate-and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia." Genome Announcements 3.6 (2015): e01347-15.. Pace, Laura A., et al. "Draft Genome of ...
This list of sequenced eubacterial genomes contains all the eubacteria known to have publicly available complete genome sequences. Most of these sequences have been placed in the International Nucleotide Sequence Database Collaboration, a public database which can be seKarched on the web. A few of the listed genomes may not be in the INSDC database, but in other public databases[verification needed]. Genomes listed as "Unpublished" are in a database, but not in the peer-reviewed scientific literature. For the genomes of archaea see list of sequenced archaeal genomes. Genome project Human microbiome project List of sequenced eukaryotic genomes List of sequenced archaeal genomes List of sequenced plastomes "Entrez Genome Database Search". National Center for Biotechnology Information. Search for details on specific genomes by organism name and strain. Schell MA, et al. (2002). "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract". Proc. Natl. ...
The draft genome of Kallotenue papyrolyticum JKG1T, a member of the order Kallotenuales, class Chloroflexia, consists of 4,475,263 bp in 4 contigs and encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The genome is consistent with a heterotrophic lifestyle including catabolism of polysaccharides and amino acids.
Maybe you thought a lot of genome papers provide "insights" - and youd be right. But did you know that even more genome papers "reveal" stuff? Its true! Heres a list of nearly 500 examples.. Abe, A., et al. (2012). "Genome sequencing reveals agronomically important loci in rice using MutMap." Nature Biotechnology 30(2): 174-178.. Acarkan, A., et al. (2000). "Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella." Plant Journal 23(1): 55-62.. Ahola, V., et al. (2014). "The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera." Nature Communications 5.. Aklujkar, M., et al. (2012). "The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features." Bmc Genomics 13.. Alcaraz, L. D., et al. (2008). "The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine ...
Experiments in animals have highlighted how specific genes in the bacterial strain may be crucial to the onset of inflammation and disease.. H. pylori is a bacterium that colonizes the stomachs of over half the worlds human population. Different strains of the bug have lived with, evolved, and followed humans on their travels since ancient times. H. pylori is now recognized as a major risk factor in the development of stomach cancer and ulcers. However, the details of what make some strains of the bug trigger disease and others not need to be fully worked out.. Martin Blaser of the New York University Langone Medical Center, one of the authors of the study, remarked: "Most sequencing efforts for H. pylori have focused on the bacterial genomes from individuals of European descent. The new sequence information helps to redress the geographic bias of earlier work and reveals important clues about the evolution and migration of the bacterium and its human host into the New World.". To help ...
Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also ...
After sequencing multiple strains of GBS, we found that eight genomes are not enough to identify all genes present in this species, and mathematical modeling made the surprising prediction that even hundreds of genomes might not be sufficient. These findings have implications for pathogenesis, vaccine design, evolution, and the concept of species and suggest that the research strategies for microbial genomes may need to be reconsidered.. The Bacterial Pan-Genome. Regression analysis showed that in the case of GBS and GAS, the bacterial pan-genome is vast because new genes continue to be added to the gene pool of the species any time a new strain is sequenced. In this view, the core genome would then represent only a small fraction of the pan-genome. This theory challenges our concept of limited variability within a bacterial species, as has been suggested recently (33), and raises the question of whether such large numbers of genes are actually available. More accurate estimates of the size of ...
Citation. Ermolaeva, M. D., White, O., Salzberg, S. L.. Prediction of Operons In Microbial Genomes. Nucleic Acids Res. 2001 Mar 01; 29(5): 1216-21.. PubMed Citation. Abstract. Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P: ,/= 0.98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site www.tigr.org/tigr-scripts/operons/operons.cgi.. ...
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen particularly associated with the inherited disease cystic fibrosis (CF). P. aeruginosa is well known to have a large and adaptable genome that enables it to colonise a wide range of ecological niches. Here we have used a comparative genomics approach to identify changes that occur during infection of the CF lung. We used the mucoid phenotype as an obvious marker of host adaptation and compared these genomes in order to analyse SNPs, indels and islands within near-isogenic pairs. In order to commence the correction of the natural bias towards clinical isolates in genomics studies and to widen our understanding of the genomic diversity of P. aeruginosa, we included four environmental isolates in our analysis. Our data suggests that genome plasticity plays an important role in chronic infection and that the strains sequenced in this study are representative of the two major phylogenetic groups as determined by core genome SNP ...
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first ...
MyJournals.org - Science - Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis (BMC Microbiology)
SCOTTSDALE, Ariz. - Whole genome sequencing - spelling out a persons entire DNA genetic code - has moved one step closer to being a medical option for direct patient care.. Physicians and researchers at Mayo Clinic in Arizona and the Translational Genomics Research Institute (TGen) successfully completed sequencing both a single patients normal and cancer cells - a tour de force of more than 6 billion DNA chemical bases.. While the whole genomes of several individuals or their cancers have been sequenced in recent years, this is believed to be among the first successful application of whole genome sequencing performed in support of the medical care of a specific cancer patient.. A male patient with pancreatic cancer was the first patient at Mayo Clinic to have whole genome sequencing performed on both his tumor and non-cancerous cells as part of a clinical research project. By comparing the tumor DNA to the patients normal DNA, researchers found genetic changes (mutations) that were important ...
Citation: N/A Interpretive Summary: The lungs of patients with cystic fibrosis (CF) can be chronically colonized by a number of bacteria. Pseudomonas aeruginosa, a common environmental bacterium, is the most prominent CF pathogen. Persistent colonization of P. aeruginosa results in progressive lung damage and is the leading cause of morbidity and mortality in CF patients. After the initial colonization, P. aeruginosa undergo changes in their genetic makeup, a process called genome evolution, which allow them to better survive in the CF lungs. One of the significant methods for genome evolution involves the uptake of large blocks of DNA from other bacteria and inserting them into their own genomes, which gives rise to genomic or pathogenicity islands. This process is called horizontal gene transfer (HGT). HGT can have a significant and immediate impact on the organisms phenotype and virulence, and therefore, it plays a significant role in bacterial genome evolution and pathoadaptation. In our ...
Arthrobacter agilis strain L77, is a plant growth promoting and cold active hydrolytic enzymes producing psychrotrophic bacterium, isolated from Pangong Lake, a subglacial lake in north western Himalayas, India. Genome analysis revealed metabolic versatility with genes involved in metabolism and cold shock adaptation, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of Arthrobacter agilis strain L77 consists of 3,608,439 bp (3.60 Mb) of a circular chromosome. The genome comprises of 3316 protein coding genes and 74 RNA genes, 725 hypothetical proteins, 25 pseudo-genes and 1404 unique genes.
Draft Genome Sequence of Kurthia huakuii LAM0618T, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry.: Kurthia huakuii LAM0618(T) is a facultati
The Genome Assembly and Annotation Team carries out "genome projects" in the classical sense, from design of the de novo sequencing strategy, on through assembly and annotation of the genome.. The team specializes in large eukaryotic genomes and transcriptomes, especially those of animals and plants. Other types of genomes analyzed include those of organelles, endosymbionts, metagenomes and metatranscriptomes, and cancer genomes. Genome assembly is not only difficult due to the sheer size of the data and computational requirements, but also because the biology of genomes is confounded by repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). The team focuses its efforts on meeting and overcoming these challenges, incorporating new technologies and developing new computational protocols as each project demands.. Annotation of the gene content of the newly assembled genome is key to understanding the genome, once finished. On this ...
A systematic study of genome context methods: calibration, normalization and combination - Background: Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results: We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack ...
We report the complete genome sequence of Corynebacterium vitaeruminis DSM 20294(T) which was identified as the producer of B vitamins in the rumen of cows. The genome of C. vitaeruminis DSM 20294(T) consists of a single replicon, the chromosome with a size of 2,931,780 bp and a G+C content of 65.53%. The genome encodes for 2,580 protein coding genes, among them those for a complete pathway to synthesize biotin. ...
Metabolic reconstruction and subsequent mathematical computation has become a useful tool in the post‐genomic era by aiding both biological computation and experimentation. In this work, we present, characterize and utilize the iAF1260 metabolic reconstruction of E. coli K‐12 MG1655. The reconstruction serves as both a BiGG database containing the current knowledge of E. coli metabolism, as well as a framework for mathematical analysis. Accordingly, the major contributions from this work are: (1) an expansion in size, scope and detail of the metabolic network of E. coli, effectively exhausting the available literature, (2) an enumeration and description of the parameters and methods needed to utilize the reconstruction as a predictive model; examples of simulation results compared with high‐throughput experimental data are presented and (3) the inclusion of thermodynamic information and a novel thermodynamic consistency analysis for chemical transformations accounted for in the ...
Molecular Characterization of Five Potyviruses Infecting Korean Sweet Potatoes Based on Analyses of Complete Genome Sequences - complete genomes;phylogenetic analyses;recombination;sweet potato viruses;
Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into
From a biological point, the rewritten genome is also interesting. Beat Christen added that- Their method is a litmus test to find out whether we biologists have correctly understood genetics, and it allows us to highlight potential gaps in our knowledge. Obviously, the rewritten genome can contain only information that the researchers have actually understood. Additional information that is situated in the DNA sequence, and has not yet been understood by scientists this information would have been lost in the process of producing the new code.. For study purposes, the scientists generated also and strains of bacteria that contained the naturally occurring Caulobacter genome segments of the new genome. By turning off certain genes in these bacteria, the researchers were able to check the functions of the genes. They tested each of the artificial genes in a multistep process.. In such experiments, the researchers found out that just about 580 of the 680 artificial genes were functional. Christen ...
With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the ...
A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A and B have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links. ...
Note to Glimmer users: it is always preferable to train Glimmer on a sample of genes from the same genome that you are finding genes in. This is easy to do with any bacterial genome, using the long-orfs program to extract long open reading frames that can be used to bootstrap the system. (This is explained in the readme files that come with Glimmer.) If you wish to search for genes in a short fragment of DNA, Glimmer needs to be trained on a longer sequence. The best strategy is to train on a closely similar genome ...
Rapid advances in the genomic sequencing of bacteria and viruses over the past few years have made it possible to consider sequencing the genomes of all pathogens affecting humans as well as the crops and livestock upon which our lives depend. The Chem-Bio Non-Proliferation program of the US Department of Energy began a large-scale effort of pathogen detection in early 2000 in an effort to provide biosecurity at the 2002 Winter Olympic Games in Salt Lake City, Utah [52, 53]. Molecular assays were developed at the Lawrence Livermore National Lab for likely bioterrorist agents by utilizing whole genome comparison methods to recognize unique regions of pathogen genomes suitable for identification. Genetic-based rapid assays were developed for all major threat list agents for which adequate genomic sequence is available, as well as for other pathogens requested by various government agencies. The assays were validated by CDC and were used at the 2002 Winter Olympics [52, 53]. The program continues ...
Our lab develops computational and experimental methods to study selection in microbes. Our computational work uses published microbial genome sequences. Vibrio species are the model experimental system for our study of adaptation to environmental stress conditions. ...
Thanks for the plug of our paper, and taking time to give us feedback. I have enjoyed the discussion this kicked up. Its a nice benefit of releasing pre-prints. I think weve covered most of whats below on twitter, but Im putting a summary here.. First, 2nd gen costs werent included in the original arXiv version of this paper, nor were 2nd gen assemblies. The primary intent of our paper is to show whats algorithmically possible with PacBio sequencing, and how long reads significantly drive down the cost of genome *finishing* and enable 1-contig assemblies. Thanks for you kind words on that, main part, of the paper! From our results, I dont think there is any debate that PacBio is much, much cheaper for genome finishing than any other approach, and is capable of some pretty cool stuff.. Adding the comparisons to 2nd gen assemblies was recently added for context; essentially, what assembly does each platform produce, at what price. You took particular exception to our $300 figure for a ...
View Notes - Lecture 2 from PLB 40175 at UC Davis. PLB 113 Lecture 2 II. Genome Organization and Gene Expression A. Plants have big (and small genomes) B. Genomes consist of single (LOW) copy and
2017-02-16 15:06:47] Checking for Bowtie Bowtie version: 2.2.8.0 [2017-02-16 15:06:47] Checking for Bowtie index files (genome).. [2017-02-16 15:06:47] Checking for reference FASTA file [2017-02-16 15:06:47] Generating SAM header for genome [2017-02-16 15:06:47] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2017-02-16 15:06:47] Mapping left_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3) [2017-02-16 15:06:47] Mapping right_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:48] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 ...
Gabriel Wu 03:42, 13 February 2013 (EST): In principle, a minimal genome that has just enough genes for a cell to grow and divide sounds good. I wonder how reliable and stable this chassis might actually be though. What if removing all the "redundant" pathways results in a fragile cell where the addition of new genes results in cell non-viability? For example, biofuel products are notoriously toxic to the cell. If a bottom up approach is taken by starting with a minimal genome and then inserting ethanol genes, the minimal genome cell will likely never grow up due to alcohol toxicity. If engineering is an iterative process, it may be difficult to optimize no growth. Sometimes its easier to start with a cell that can tolerate small amounts and then knock in or out whichever genes are needed to improve tolerance. ...
ABSTRACT: BACKGROUND: Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts.$\backslash$n$\backslash$nRESULTS: We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All ...
Weissella cibaria KACC 11862 is a Gram-positive, heterofermentative, Leuconostoc-like lactic acid bacterium that is widely distributed in Korean traditional foods such as kimchi. Here we report the draft genome sequence of the type strain, W. cibaria KACC 11862 (1,599 known genes, 80 RNA genes), which consists of 72 large contigs (|100 bp in size).
The Bacterial Genome Subtraction Kit offers an effective method for comparing bacterial genomes. It enables identification of genomic DNA differences between two strains.
The Bacterial Genome Subtraction Kit offers an effective method for comparing bacterial genomes. It enables identification of genomic DNA differences between two strains.
... The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system developed by the DOE-Joint Genome
Whole genome sequencing (WGS), which is the process of determining an organisms complete DNA sequence, can be used to identify DNA anomalies that cause disease. Identifying disease-causing DNA abnormalities allows clinicians to better predict an effective course of treatment for the patient.
Conclusions The reconstruction of short term genome dynamics events shows that microbial genomes exist in a state of perennial flux, gaining, losing, expanding and contracting gene families. Typically, genome dynamics processes are rapid, with gains and losses of multiple gene families occurring within the time frame of a single nucleotide substitution per gene. Thus, gene flux is the dominant mode in microbial evolution such that microbes primarily differ from each other on the scale from static to highly dynamic. The rates of gene family gain and loss in most microbial groups are approximately an order of magnitude greater than the rates of expansion and contraction of pre-existing families, indicating that HGT is the principal source of new genes in prokaryote evolution. Overall, gene family loss notably prevails over gain, i.e. evolving genomes appear to spend more time contracting than expanding. It seems most likely that the gradual gene loss is compensated for by episodes of rapid gene ...
Hello,. The Tuxedo tool suite is tuned for mammalian genomes and is probably not the best choice. There are many publications that tackle the subject (google or other pub search).. I suggest reviewing the latest publications, comparing against the tools available in the Tool Shed, then creating your own pipeline. If there is a particular tool that you want to use that isnt already wrapped for Galaxy, it could be, if you are able to do that or have informatics resource to help.. Thanks, Jen, Galaxy team. ...
View Notes - Biology 1201 from BIOL 1201 at LSU. Eucaryotic Gene Regulation Genome Structure, Genes, DNA, and chromosomes Complete Genome DNA sequence know humans ,chimps ,flies ,worms, and plants…
In this tutorial we will screen genome sequences of Escherichia coli samples for phenotypic traits using the E. coli functional genotyping plugin. This plugin contains public databases for serotype, virulence and resistance prediction, as well as plasmid and prophage detection. An in silico PCR tool is also implemented, making it possible to detect Shiga toxin gene subtypes
The NIH is now accepting applications for the Somatic Cell Genome Editing (SCGE) program. The SCGE program aims to improve genome editing technologies to accelerate the translation of this technology into clinical applications and maximize the potential to treat as many diseases as possible. Pending the availability of funds and sufficient numbers of meritorious applications, the NIH expects to fund projects to provide better animal models for assessing genome editing in vivo, tools and assays to detect adverse consequences of genome editing in human cells, new technologies to deliver genome editing machinery into disease relevant cells and tissues in vivo, novel genome editing and engineering systems, and a Dissemination and Coordinating Center. Applications are due April 3, 2018. For additional information on these RFAs visit our Funding Opportunities page.. ...
White Paper: Seven Bridges Genomics and Intel test the performance of an Intel® Xeon® processor E5 v3 family-based whole genome analysis solution.
Comparative assembly using multiple genomes.The target genome is shown in the center, aligned to two related genomes, A and B. The DNA sequence of the target di