TremaGene : tremagene

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TremaGene Database Search - Search our collection of genes and transcripts

Instructions specific to this page

TremaGene can be searched using IPR, GO and/or KO id filters. First click on the [+] Expand label for the Species selection section and select 1 or more species to start your query. Note that if you select no species from the list, your query will be applied to all species in TremaGene (depending on the complexity of your query, this may take a long time to complete). After selecting the species to focus on, open the sections below to set specific filters you'd like to apply. You're able to request a specific gene name (or comma-delimited list of gene names), orthologous group name if such is available, IPR id, GO term and/or KO id. You are allowed to enter comma-delimited lists of any of those ids as well. Note that filtering on multiple ids of a single type will return genes/transcripts annotated by any of those ids. But if you set filters using 2 or more id types (i.e. IPR id + KO id), each gene or transcript returned will be required to have at least one id from each list you supplied.

You will then arrive at a page showing the slice of data you've retrieved from TremaGene. The Query Definition section now displays the query you made to extract the results below. Then the Data Download section allows you to download the full fasta for all the genes/transcripts you requested. Note that if the type of fasta you request (nucleotide or protein) doesn't exist for any of the genes or transcripts in your list, the output file will still display the gene name(s) as headers, but the sequence record for those will be empty. The Results section will list all the genes and/or transcripts in your return set, organized by species, then by group if available (typically groups built by software such as orthomcl or inparanoid). Each gene or transcript name is a link that will take you to a final detail page showing the available annotations for that entity. You will also be able to download that single entity, or forward its sequence into TremaBlast for further analysis. For more information on TremaGene and the available annotations see the TremaGene FAQ.

How to use this page

Access into the TremaGene database frequently comes from other tools within the site such as the contig links from TremaPath which directly jump to the details pages that are the terminus of a TremaGene search, or from associated external sites. But the TremaGene Database Search tool can also be used to extract custom slices of our database using available annotations. This tool is also very useful for retrieving the full protein or nucleotide fasta of our genesets, or of the slice you define, using the appropriate Download links.

Query Definition
Please setup your query in the expandable sections below
Species selection
Use this table to select which species you want reported to you. Choice of species is the top level filter you will set. Other selections you make below will only report results from the species you selected. If you do not select a species, TremaGene will build results based on all available species.

Selecting many or all available species may cause this service to hang or crash depending on server load. We strongly suggest limiting searches to 5 species or less. But note that applying ANY filter will drastically improve query speeds. So searches for small collections of IPR ids, GO terms and/or KO ids across all species should complete without issue.

Species listed in RED have stage or tissue specific gene expression annotation available. Expression values for a gene are provided in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) per stage/tissue based on available RNAseq experiments.

(PC/UNIX/Linux users use control- and/or shift- click to select multiple species, MAC users use command- and/or shift- click)
Filter selection
This section allows you to request a specific slice of the TremaGene database for the species you've selected above. You can filter using gene names, group ids for gene families, IPR, GO or KO annotations and then generate a report on the returned gene(s) including primary sequence (protein and/or nucleotide) as well as available annotation.

*note: When searching for GO terms, please be aware that NemaGene only tracks the highest resolution GO term assignment for genes/transcripts. You cannot choose a root term such as GO:0008150 (biological process) and have all GO terms under that root term returned to you.

Gene or Transcript name: 
Group name: 
IPR id:(eg. IPR006186)
GO id:(eg. GO:0016787)
KO id:(eg. K06269) v1.0(AWS)     Copyright Statement
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