Pathema also offers single-genome and comparative multi-genome analyses as well as display tools at the genome, gene, and pathway level for these pathogens as well as display tools at the genome, gene, and pathway level for these pathogens.
The Pathema - Entamoeba will be updated every two months with the latest annotation and newly sequenced genomes.
|All genomes sequenced at TIGR are initially assigned
annotation through an automated process. Names and functional
annotation are then manually
curated. As direct experimental evidence rarely exists for each
gene in a sequenced organism, name assignments are usually based on
sequence similarity. Therefore, all TIGR name assignments
should be regarded as provisional. We strive to annotate each
gene with as much information as we can confidently impart, but are
also wary of inferring too much from sequence similarity. We
prefer to err on the side of caution and we have devised a nomenclature
scheme that reflects our degree of confidence in a particular
We encourage feedback from the community to help identify errors or to provide suggestions to improve the annotation of our genes.
All tables on Pathema - Entamoeba have a "Download" button allowing the user to open the table in a tab delimited format, this can then be exported to a spreadsheet program like Excel. In addition, all graphics shown on Pathema - Entamoeba have links allowing the user to see the underlying data in table format. An "Options" button also appears if the tool being used has any additional options such as downloading a FASTA file of all genes shown or changing the annotation type displayed. As new Pathema - Entamoeba tools are developed, they can easily be added to this Options menu. Each page on the Pathema - Entamoeba also contains an information icon "i" which opens up a small window with a description of the page. Finally, throughout Pathema - Entamoeba whenever a selection box with many options is encountered search boxes and tree views are available to sort quickly through the data based on a string search or taxonomic classification.
Welcome to Pathema - Entamoeba. This section of the Manual will help get you started using Pathema. It will cover the most efficient and easiest ways to retrieve the data that's most important to you. If you have any questions regarding the site please check the FAQ section. If your questions are still not answered please feel free to contact us so that we may assist you.
Please choose the following topic that best describes what you're looking for.
To make finding the necessary tool easier, The Comparative Tools List is organized into different categories.
The comparative tools are based on All vs. All data. All of the proteins are routinely blasted against one another. We call these the "All v/s All" searches. When a new genome is added to the database the all v/s all searches are re-run. The information from the All v/s All blast searches is displayed thoughout Pathema - Entamoeba.
On each gene page you will see Click here to submit new annotation for this gene. Clicking that link will take you to a form where you will be able to enter your own annotation. Once you submit your changes your annoation will be shown on the Gene Page.
Note: When navigating through Pathema - Entamoeba clicking on an organism's name will take you to that organism's genome page.
In addition just hovering over the tab will produce a drop down of all tools available under that section. This allows for quick access if you know exactly what tool you want to use.
Each gene found in Pathema - Entamoeba has it's own Gene Page. The Gene Page provides users information pertaining to a specific gene such as the Locus Name, Gene Symbol, Coordinates, DNA Molecule Name, Gene Length, JCVI Cellular Role Catgeory and much more. The Gene Pages also provide gene speficic tools. These tools are found on the left side of the Gene Page. Examples of tools provided are a Gene Graphic, Protein vs. All Alignment, TmHMM Information, TIGRFAM & Pfam Matches, Paralog Information, Ribosomal Binding Site Information, GC Content Display, and Region View.
Located at the top of each Gene Page is it's Primary Locus if available. If a Primary Locus exsists clicking on the name will take you to another Gene Page containing the original sequencing center's information. Links to the gene's NCBI Genbank Page and it's Swiss-Prot Page are also available at the top of the page.
There are currently four different ways to quickly locate your gene of interest.
Note: When navigating through Pathema - Entamoeba clicking on a gene locus will also take you to that specific gene page.
The Gene Cart allows users to preselect a set of genes of interest. Genes of interest can be added from any page that displays a table of genes, such as search results, resulting gene tables from toolbox and comparative analyses tools, and gene lists. Selected genes can be viewed and downloaded from the Gene Cart page. In addition, any gene cart genes found in any graphical results from comparative analyses and toolbox tools will automatically be highlighted. Cookies must be enabled to use this tool. The cart holds a maximum of 300 genes at once.
You can always see what genes you have selected by visiting the Gene Cart.
What browser does Pathema work best on?
Pathema works best on Firefox. This is the
browser that we do most of our testing on. Pathema does work
on Internet Explorer but for best results we encourage the use
When I look at the All vs All results for my protein, it is showing the self hit at less than 100%, why is that?
When we run the All vs All blastp searches we use the seg+xnu
filters to mask off segments of the query sequence that have low
compositional complexity, as determined by the SEG program of
Wootton & Federhen (Computers and Chemistry, 1993), or segments
consisting of short-periodicity internal repeats, as determined
by the XNU program of Claverie & States (Computers and Chemistry,
1993). Filtering can eliminate statistically significant but
biologically uninteresting reports from the blast output (e.g.,
hits against common acidic-, basic- or proline-rich regions),
leaving the more biologically interesting regions of the query
sequence available for specific matching against database
sequences. Using these filters will cause the low complexity
regions of the query sequence to appear as "XXXX", and it will
then not "hit" the same region in an identical protein, giving
you a %identitiy of less than 100%.
Where can I obtain Genomic DNA or strains?
Unfortunately JCVI does not have any Genomic DNA or strains to
provide to the public. We only keep the sequence data, not the
actual organisms or DNA. Please contact the ATCC if you wish to obtain Genomic
DNA or strains.
Is there a way to preselect genomes or genes of interest?
Yes. Pathema offers a Gene and Genome Cart. These carts are located
under the Carts tab in the header.
Once the Genome Cart
has been set, other selection boxes for genomes in the
Pathema (list of genomes in any search tools, toolbox tools,
comparative analyses tools, and gene lists) will automatically
only display this list of preferred genomes.
Genes can be added to the Gene Cart
from any page that displays a table of genes, such as search results, resulting gene tables from toolbox and
comparative analyses tools, and gene lists. Selected genes can be viewed and downloaded from the Gene
Cart page. In addition, any gene cart genes found in any graphical results from
comparative analyses and toolbox tools will automatically be highlighted.
Cookies must be enabled to use this tool. The cart holds a maximum of 300 genes at once.
Where can I find help for a specific page or tool?
All tools have an information button located next to the title on
the specific page. The information button is an "i" inside a
circle and clicking on this button will produce a popup
containing specific information on how to use the page or tool.
What download tool should I use?
Use this tool to download sequences to your local disk.
Gene Attribute Download: Use this tool if you would like selected gene attributes for either a user-generated list of genes or all genes from a specific organism and/or role category.
Pathema FTP: The FTP site contains all the Pathema databases in the .gff format.
What is the difference between hypothetical, unknown, and unclassified genes?
Hypothetical genes lack significant sequence similarity to
characterized or uncharacterized genes from other organisms. Unknown genes do have significant sequence similarity
to genes from other organisms, but the function or biological role of the protein is unknown. Unclassified genes have not been
assigned a JCVI role id.
What is the difference between conserved hypothetical and hypothetical genes?
Hypothetical genes lack significant sequence similarity to
characterized or uncharacterized genes from other organisms. Conserved hypothetical proteins have sequence
similarity only to hypothetical proteins from other organisms. They are not members of a defined family, lack
significant similarity to defined protein motifs, and there is no evidence from which to infer either their function or
Can you provide me with medical advice on a disease found on Pathema?
JCVI is not qualified to offer medical advice. For more
information on a specific disease found on Pathema please contact
the Centers for Disease Control and Prevention, the
World Health Organization, or go to your local doctor.
What's the difference between Primary Annotation and JCVI Annotation?
The sequencing center's annotation is called the "Primary annotation" and the automated annotation done while the genome is
being loaded into Pathema is called the "JCVI annotation". Genomes sequenced at JCVI have only one set
of annotation so the "Primary" and "JCVI" annotation are the same.
What is the Annotation Service?
The Annotation Service allows users to send us a prokaryotic genomic sequence
and we return to the user both the automated annotation for the sequence and our manual annotation tool Manatee. The users can
then go on to manually annotate their genome. The Annotation Service is offered free-of-charge by JCVI to any interested
researcher who has a bacterial or archaeal DNA sequence to annotate. All data generated from an Annotation Engine user's
genome is kept separate from other JCVI data to retain confidentiality.
Does JCVI offer a class where I can learn more about their annotation process and Pathema?
Yes, JCVI does offer a three-day course in Prokaryotic Annotation
and Analysis. For more information on this course and upcoming
dates please click here.
Available under the Downloads menu are the Batch Download and the Gene Attribute Download. The Batch Download allows users to get a FASTA file of the nucleotide or protein sequence for a set of genes. The Gene Attribute Download allows users to download over 20 different gene attributes (i.e. coordinates, gene symbol, product name, EC#, GenBank ID, etc.) for a set of genes. To select genes for these tools the user can upload a list of genes or select all genes from an organism and/or role category.Batch Download: