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SLiMSuite: Short Linear Motif discovery and molecular evolution toolkit

EdwardsLab Servers

Many of the EdwardsLab servers are currently under development. Please see the SLiMSuite Blog and REST server news page for more information and updates.

Servers

SLiMSuite-REST

RShiny

WebApollo

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Server Home REST Servers RShiny Servers WebApollo Genomes Bioware@UCD

Web Apollo Genome Servers

Genome projects involving the Edwards Lab are available at our Web Apollo Genome server for browsing and annotation. User login may be required for unpublished genomes - please get in touch if you would like to gain access and/or be involved in genome annotation. Genomes available through these servers can be searched using the BLAST tool, below. A password may be required for searching genomes that are not marked as public.

Currently, public genome browsers are available for our two snake genome, sequenced as part of the BABS Genome Project, and the invasive cane toad, Rhinella marina:

BrownSnake

TigerSnake

CaneToad

Eastern Brown Snake v1.0 Tiger Snake v1.0 Cane Toad v2.2

Other genome projects we are involved in, include:

  • Multiple (haploid and diploid) Saccharomyces cerevisiae yeast strains.
  • A novel, dichloromethane and quaternary amine fermenting bacterium (Peptococcaceae, strain DCMF).
  • Mixed bacterial genome samples from marine and polar environments.
  • Various bacteriophage
  • Assembly of the Rock wallaby and Eastern Bettong, as part of the Oz Mammals Genomics project.

Web Apollo Genome search tool

This server allows simple Exonerate or BLAST+ searches of DNA, CDS or protein sequences against one of our Web Apollo genomes. Select the genome to search and the Web Apollo instance to generate links for. Optionally, tracks to display can be listed under Advanced Options. Private genomes will need a password for access. This password will also be required to access the REST server results.

Note: some genomes may have multiple Web Apollo annotations. It is the genome status, not the Apollo status that determines password requirements. If no Web Apollo ID is selected, no links table will be generated - other search results will still be returned.


Search Genome: WebApollo ID: Password:

CDS, DNA or protein sequences to search against genome (fasta):
Search method: | Max number of hits returned:

Paste fasta format sequence(s) into text box:

Alternative fasta file upload:

Check/set options below, then click:

After running, click on the html tab to see the summary table of hits with Web Apollo links.

This server is still in development. Please report any odd/unwanted behaviour.

BLAST+ Search Options

NOTE: if no hits are returned, try reducing the min local alignment %identity.

E-Value cut-off for BLAST searches:
Min local alignment length:
Min local alignment %identity:

Advanced Options

List of tracks to display in Web Apollo browser:

Other options:


© 2018 RJ Edwards. Contact: richard.edwards@unsw.edu.au.