Frequently Asked Questions
BLAST
Genome Browser
View a Gene Page
Fetch a Scaffold
Pfam Domains
Developmental Expression
Download Sequences
Database Statistics
Miscellaneous
What version of BLAST is implemented in the Hydractinia BLAST tool?
We use SequenceServer, which implements the NCBI BLAST+ 2.10.1+ 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 both Hydractinia species are listed here: https://research.nhgri.nih.gov/hydractinia/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
Hydractinia JBrowse genome browser (B), the scaffold Fetch tool (S), the WikiGene pages (G).
What tracks are available for viewing in the Hydractinia genome browser?
- Detailed descriptions of genome browser tracks for both Hydractinia species are listed here: https://research.nhgri.nih.gov/hydractinia/jbrowse/
How can I navigate the Hydractinia 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 Hydractinia genome browser searchable?
The genome browser is currently searchable using
Hydractinia scaffold (
e.g., HyS0100, HyE0002) or gene (
e.g., HyS0459.4, HyE0001.10) identifiers.
Is there a preferred Web browser I should use to view the Genome Browser?
The
Hydractinia 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.
How do I search for a gene using the Hydractinia gene Wiki pages?
The
Hydractinia gene Wiki pages are accessible from the home page left sidebar and are searchable by entering a
Hydractinia gene identifier (
e.g., HyS0001.4, HyE0208.10) in the search box and clicking ‘Go’.
What type of information is available in the Hydractinia gene Wiki pages?
Each record in the gene Wiki pages represents a single
Hydractinia gene and provides the following annotation: nucleotide and protein sequences, coding exonic genomic coordinates, pre-computed BLAST hits from numerous organisms displaying the top hits for each protein, InterProScan data, PFAM domains, functional annotation (gene ontology derived from Argot2.5 and PANNZER2), developmental expression data, related human disease genes from the Online Mendelian Inheritance in Man (OMIM) database, and ortholog clusters inferred using the Orthofinder2 pipeline.
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., HyS0325, HyE0030) in the "Fetch Scaffold" textbox to return a single FASTA-formatted
Hydractinia 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., HyS0325, HyE0030) 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.
What options are available for searching the Hydractinia genomes for Pfam-A domains?
You can elect to search the
H. symbiolongicarpus or
H. echinata Protein Models, 6-frame translations of scaffolds, or both. You may either select a domain name or domain accession number from the drop-down menus, or enter a domain name or five-digit Pfam accession number in the search box.
How were Pfam domains identified in the Hydractinia genome?
We used hmmscan from the HMMER suite to search the
Hydractinia Augustus Protein Models and the six-frame translations of the
Hydractinia genomes for domains from the Pfam-A database (version 31). We filtered the hmmscan output using an e-value cutoff of 1e-6. For more information on Pfam, visit
http://pfam.xfam.org/.
What is the structure of the definition line when sequences are downloaded from the Pfam-A domains page?
If the "Full-length protein sequences, in FASTA format" option is chosen, the definition line will contain the gene identifier. If the "Pfam-A domains of selected proteins, in FASTA format" option is chosen, the definition line will contain the gene identifier, the coordinate range of the domain in that protein model, and the name of the query domain.
What is the source of the developmental expression data?
Three replicate RNA-seq samples were collected at four different time points during
Hydractinia symbiolongicarpus embryonic development: at the 4-cell, 16-cell, and 64-cell stages and from 24-hour larvae. Each replicate consisted of pools of embryos or larvae from a single spawning event resulting from a cross of the 291-10 male strain with the 295-10 female strain. RNA-seq libraries were constructed for each sample for a total of 12 libraries. These libraries were then sequenced on the Illumina HiSeq 4000 platform using indexed 75-base paired end reads. Sequence reads were processed and aligned to the
H. symbiolongicarpus gene models, counted, and normalized via MedianNorm
(Anders and Huber, 2010).
Where can I download the full Hydractinia genome assemblies?
The full genome assemblies, consisting of 4,840 (HyS) and 7,767 (HyE) 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., HyS
XXXX) are named as follows:
- HyS = Hydractinia symbiolongicarpus and HyE = Hydractinia echinata.
- XXXX = padded integer between 0001 and 4840 for HyS and 0001 and 7767 for HyE.
How are the gene identifiers generated?
Genes (
e.g., HyS
XXXX.NNNa) are named as follows:
- HySXXXX = corresponds with the scaffold where the gene is located.
- NNN = non-padded integer. It is unique in combination with the scaffold ID. It is usually in order of its most 5' position on the scaffold, but is not a requirement. Newly added genes get the next highest unused integer regardless of its position.
What functional annotation is available?
GO term functional annotation is available from both Argot2.5 and PANNZER2 with the best BLAST hit listed in the 'GO-terms' file.
Where can I find information regarding Hydractinia data type summaries?
Clicking the ‘Database Statistics’ link on the Portal side bar displays the
Hydractinia database statistics table page detailing the data types (e.g. Gene Models) and total number of database entries for each species.
How should data derived from the Hydractinia Genome Project Portal be cited?
Please cite this Web site:
https://research.nhgri.nih.gov/hydractinia/
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 Hydractinia Genome Project?
For additional information, comments, or questions regarding the
Hydractinia Genome Project, please contact Dr. Baxevanis directly, at andy@nhgri.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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