Frequently Asked Questions
BLAST
Genome Browser
Single-Cell Browser
View a Gene Page
Fetch a Scaffold
Download Sequences
Miscellaneous
What version of BLAST is implemented in the Hydra AEP BLAST tool?
We use SequenceServer, which implements the NCBI BLAST+ 2.11.0+ command line applications (referred to as the BLAST+ applications). SequenceServer (version 1.0.14) is provided by the Wurm Lab and subject to all
Terms & Conditions set forth by the developers.
What BLAST programs are available?
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares an amino acid query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
What BLAST databases are available?
Descriptions of nucleotide and protein databases for
Hydra AEP,
Hydra oligactis and
Clytia hemisphaerica are listed here:
https://research.nhgri.nih.gov/HydraAEP/databases.shtml
What do the boxes in the 'Links' column of the BLAST output represent?
The 'Links' column provides clickable hyperlinks for each significant BLAST alignment to their entries in the
Hydra AEP JBrowse genome browser (B), the scaffold Fetch tool (S), the WikiGene pages (G), and the Transcript pages (T).
What tracks are available for viewing in the Hydra AEP genome browser?
Detailed descriptions of genome browser tracks for both
Hydra species are listed here:
https://research.nhgri.nih.gov/HydraAEP/jbrowse/
How can I navigate the Hydra genomes using JBrowse?
A user can zoom in or out and left or right on a region of interest by clicking on the appropriate icons centered on the blue toolbar. In addition, available tracks can be viewed (or hidden) by clicking on the appropriate track label on the left sidebar of the browser window.
Is the Hydra AEP genome browser searchable?
The genome browser is currently searchable using
Hydra AEP and
Hydra oligactis scaffold (
e.g., HVAEP15, HOLI00035) or gene (
e.g., HVAEP1.G000001, HOLI00740.G12320) identifiers.
Is there a preferred Web browser I should use to view the Genome Browser?
The
Hydra AEP Genome Project Web site was developed and tested using Google Chrome. The rendering of desired output while using other Web browsers, including Firefox, Safari and Internet Explorer, is assumed but not guaranteed.
What type of information is available in the Hydra AEP Single-Cell Browser?
The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We used Drop-seq to sequence the transcriptomes of 24,985 single Hydra cells to uncover the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. This Single-Cell portal presents these data in an interactive format, and allows for visualization of sequencing statistics, clustering results, and gene expression across every cell in our dataset.
What tool was used to implement the Hydra AEP Single-Cell Browser?
The
Hydra AEP Single-Cell Browser was implemented with ShinyCell (
https://github.com/SGDDNB/ShinyCell).
How do I search for a gene using the Hydra AEP gene Wiki pages?
The
Hydra gene Wiki pages are accessible from the home page left sidebar and are searchable by entering a
Hydra gene identifier (
e.g., HVAEP1.G000001, HOLI00740.G12320) in the search box and clicking "Go".
What type of information is available in the Hydra AEP gene Wiki pages?
Each record in the gene Wiki pages represents a single
Hydra gene and provides the following annotation: scaffold, transcripts, nucleotide and protein sequences, coding exonic genomic coordinates, pre-computed BLAST hits from numerous organisms displaying the top hits for each protein, InterProScan data, ortholog clusters inferred using the Orthofinder2 pipeline, and links to several browsers.
How are the phylogenetically informed ortholog clusters determined?
Orthologous clusters of proteins were inferred using the Orthofinder2 pipeline (Emms and Kelly 2015, 2018).
How do I download a single genomic scaffold sequence?
A user can enter a ScaffoldID (
e.g., HVAEP15, HOLI09985) in the "Fetch Scaffold" textbox to return a single FASTA-formatted
Hydra AEP or
Hydra oligactis scaffold sequence.
Is there a way to download a partial scaffold sequence?
A partial scaffold sequence can be retrieved by entering a ScaffoldID (
e.g., HVAEP15, HOLI09985) while also specifying the relative beginning and ending coordinates in the "Fetch Scaffold" textbox.
What are the other options for fetching a scaffold sequence?
A user can optionally retrieve either a reverse complement or the six-frame translation of a scaffold or partial scaffold by selecting the appropriate "Fetch Scaffold" search option.
Where can I download the full Hydra AEP and Hydra oligactis genome assemblies?
The full genome assemblies, consisting of 15 (HVAEP) and 16,314 (HOLI) scaffolds respectively, are available for download from the sidebar "Download sequences-->Genome Assembly" search option.
What is the convention used for naming scaffolds?
Scaffolds (
e.g., HVAEP
X, HOLI
X) are named as follows:
- HVAEP = Hydra vulgaris AEP and HOLI = Hydra oligactis.
- XXXXX = non-padded integer between 1 and 15 for HVAEP and padded integer between 00001 and 16314 for HOLI.
How are the gene identifiers generated?
Genes (
e.g., HVAEP1.G000001, HOLI01379.G4366) are named as follows:
- HVAEPX, HOLIX = corresponds with the scaffold where the gene is located.
- GNNNNNN = leading G (gene) with a padded gene number (for Hydra AEP) and a non-padded gene number (for Hydra oligactis). The gene number identifier is unique in combination with the scaffold ID.
How should data derived from the Hydra AEP Genome Project Portal be cited?
Please cite this Web site:
https://research.nhgri.nih.gov/HydraAEP/
How can I contact the Web site administrator regarding technical issues?
Please send any Web site usability or technical correspondence to bioinformatics@nhgri.nih.gov.
Where can I get additional information about the Hydra AEP Genome Project?
For additional information, comments, or questions regarding the
Hydra AEP Genome Project, please contact Dr. Baxevanis directly, at andy@mail.nih.gov.
How frequently are the data and portal tools updated?
Changes to the Web site and underlying data are documented in the
Release History.
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