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HelmCoP : ortholog search

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[June.7.2017]   
Bioinformatics Workshop for Helminth Genomics (2015) class materials now freely available!

[May.11.2017]   
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HelmCoP ortholog search - Build ortholog based custom queries against the HelmCoP database

How to use this page

This page gives the user access to orthology and homology information for genes of interest. The database of helminth proteomes is the most comprehensive available to date with 38,776 orthologous groups from 18 species. Orthology was inferred using OrthoMCL (Li, L Genome Res. 13:2178-2189). The user can require that a certain species be included in an orthologous group, while excluding another species from a search, enabling the user to isolate groups of proteins found in a select group of species. HelmCoP can also be searched using GO annotations, KEGG orthology (KO), and Interpro domains. Essentiality can also be used in the search to find genes that have RNAi phenotype, based on association with C. elegans genes. Genes with a PDB structure, signal peptide and a particular DrugBank ID can also be found. Further, HelmCoP can be searched for genes that are potential vaccine candidates. HelmCoP also provides extensive annotation of included proteins (see chart at the bottom of this page). Using orthology, annotation can be carefully expanded to other proteins in an orthologous group, yielding many new insights into proteins with limited information. The page provides insights into gene duplications, deletions, and insertions. This page is particularly useful for comparative genomics and drug discovery. Output is originally displayed in HTML format, but a tab-delimited version of your query output is available via the Full Results Download button at the top of the results page. Please refer to the HelmCoP FAQ for additional information.

Due to the size of the database and the complexity of some queries, HelmCoP limits HTML output to the first 20000 rows* returned by your query. Full results are only available via the Full Results Download button in the case of queries resulting in more than 20000 rows*. Some extreme queries may be refused to prevent a page time-out, but in this case you will be prompted with the most 'expensive' portion of your query. In many cases simply removing the specified 'expensive' filter can result in a manageable output.

*Result sets truncated at 20000 rows do not consistently reflect orthologous group members! Use the Full Results Download button to download the complete, tab-delimited output of your query to be sure you are seeing the full composition of orthologs returned by your query.

Ortholog

Ortholog species composition
*Note that you must INCLUDE at least one species in your query
*Note that non-worm species are only annotated with drugbank, PPI, orthology assignments and PDB information

Species
Include
Exclude
Do not filter on this

Parasitic Nematodes

Free-living Nematodes

Platyhelminthes

Hosts/Outgroups


Function


Essentiality

Structure

Signal peptide


Drugs


(check box to filter out genes that are not listed as druggable targets)


Vaccine candidates






Output options

Data availability notice

Not all analysis annotations are available for all organisms. Selecting filters or outputs that don't exist for your chosen organism(s) can produce empty result sets. Please refer to the table below to see which species have which annotations avaible to query.




 
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