Search For Gene by gene name

Select an organism :

  Name of the gene :  
Input Format : gene_prefix+geneId e.g: Albla_Nc14125180

Name of the Organism Gene Prefix Examples
Aphanomyces invadans Aphin_ Aphin_H310_13904
Aphanomyces astacii Aphas_ Aphas_H257_00053
Hyaloperonospora arabidopsidis (Emoy2) Hyaar_Emoy2 Hyaar_Emoy2800014
Albugo laibachii Albla_Nc14 Albla_Nc14000370
Phytophthora cinnamomi Phyci_ Phyci_331428
Phytophthora infestans T30-4 Phyin_T30-4 Phyin_T30-4PITG_00006
Phytophthora parasitica INRA-310 Phypa_INRA-310 Phypa_INRA-310PPTG_00014
Saprolegnia parasitica CBS223.65 Sappa_CBS223.65 Sappa_CBS223.65SPRG_00054
Phytophthora ramorum Phyra_ Phyra_93231
Phytophthora sojae Physo_ Physo_127034
Phytophthora capsici LT1534 Phyca_LT1534 Phyca_LT1534524845
Saprolegnia diclina VS20 Sapdi_VS20 Sapdi_VS20SDRG_00040
Pythium ultimum DAOMBR144 Pytul_DAOMBR144 Pytul_DAOMBR144PYU1_G000552
Pythium iwayamai DAOM 242034 Pytiw_DAOMBR242034 Pytiw_DAOMBR242034maker-piw_contig_1-fgenesh-gene-0.12
P. ultimum var. sporangiiferum Pytul_var.sporangiiferum Pytul_var.sporangiiferummaker-pug3_contig_1-fgenesh-gene-0.38
Pythium arrhenomanes ATCC 12531 Pytar_ATCC12531 Pytar_ATCC12531maker-par_contig_1-snap-gene-1.7
Pythium aphanidermatum DAOM BR444 Pytap_DAOMBR444 Pytap_DAOMBR444maker-pag1_scaffold_1-snap-gene-0.65
Pythium irregulare DAOM BR486 Pytir_DAOMBR486 Pytir_DAOMBR486maker-pir_contig_1-snap-gene-1.28
Pythium vexans DAOM BR484 Pytve_DAOMBR484 Pytve_DAOMBR484maker-pve_contig_1-snap-gene-1.28
Phytophthora agathidicida Phyag_ Phyag_g16
Phytophthora kernoviae Phyke_ Phyke_g158
Phytophthora pluvialis Phypl_ Phypl_g12
Phytophthora multivora Phymu_ Phymu_g6
Phytophthora taxon totara Phyta_to_ Phyta_totarag5
Plasmopara halstedii Plaha_ Plaha_PHALS_12045

Search for gene by primary annotation

    Select an organism :
      1. Albugo laibachii Nc14 (V1)
      1. Phytophthora agathidicida (V1)
      2. Phytophthora capsici LT1534 (V1)
      3. Phytophthora cinnamomi (V1)
      4. Phytophthora infestans T30-4 (V1)
      5. Phytophthora kernoviae (V1)
      6. Phytophthora multivora (V1)
      7. Phytophthora parasitica INRA-310 (V1)
      8. Phytophthora pluvialis (V1)
      9. Phytophthora ramorum (V1.1)
      10. Phytophthora sojae (V1)
      11. Phytophthora sojae (V5)
      12. Phytophthora taxon totara (V1)
      1. Plasmopara halstedii (V1)
      1. Pythium vexans DAOMBR484 (V1)
      1. Hyaloperonospora arabidopsidis Emoy2 (V8.3)
      1. Pythium aphanidermatum DAOMBR444 (V1)
      2. Pythium arrhenomanes ATCC12531 (V1)
      3. Pythium irregulare DAOMBR486 (V1)
      4. Pythium iwayamai DAOMBR242034 (V1)
      5. Pythium ultimum var.sporangiiferumBR650 (V1)
      6. Pythium ultimum DAOMBR144 (V1)
      1. Saprolegnia diclina VS20 (V1)
      2. Saprolegnia parasitica CBS223.65 (V1)
      1. Aphanomyces astaci (V1)
      2. Aphanomyces invadans (V1)


    Primary annotation name :  
primary annotations are derived from the blast hits of the protein sequences with nr database having > 50% identity over 50% of the query length. If the first hit matches with a un-named protein product, then the annotation of the subsequent qualified hit is assigned as the primary annotation for the query sequence.
Input Example: Transcript keyword: actin

Search By Genome Location

    Select an organism :

    Enter Genome Location :  
Input Format: Scaffold_name:location_start-location_end. e.g: Scaffold_2:4000-50000
A genome query returns the documented features present in the query location with clickable links.

Search for conserved regions

    Select an organism :

    Enter Genome Location :  
This query results in listing out all other oomycetes genomes that has a good matching region to the query genome location. The target regions on click leads to an output similar to Genome Location query.
Input Format: Scaffold_name:location_start-location_end. e.g: Scaffold_2:4000-50000

Search By Pathway

    Select an organism :
      1. Albugo laibachii Nc14 (V1)
      1. Phytophthora agathidicida (V1)
      2. Phytophthora capsici LT1534 (V1)
      3. Phytophthora cinnamomi (V1)
      4. Phytophthora infestans T30-4 (V1)
      5. Phytophthora kernoviae (V1)
      6. Phytophthora multivora (V1)
      7. Phytophthora parasitica INRA-310 (V1)
      8. Phytophthora pluvialis (V1)
      9. Phytophthora ramorum (V1.1)
      10. Phytophthora sojae (V1)
      11. Phytophthora sojae (V5)
      12. Phytophthora taxon totara (V1)
      1. Plasmopara halstedii (V1)
      1. Pythium vexans DAOMBR484 (V1)
      1. Hyaloperonospora arabidopsidis Emoy2 (V8.3)
      1. Pythium aphanidermatum DAOMBR444 (V1)
      2. Pythium arrhenomanes ATCC12531 (V1)
      3. Pythium irregulare DAOMBR486 (V1)
      4. Pythium iwayamai DAOMBR242034 (V1)
      5. Pythium ultimum var.sporangiiferumBR650 (V1)
      6. Pythium ultimum DAOMBR144 (V1)
      1. Saprolegnia diclina VS20 (V1)
      2. Saprolegnia parasitica CBS223.65 (V1)
      1. Aphanomyces astaci (V1)
      2. Aphanomyces invadans (V1)


    Enter KEGG ID :  
This is one of the nicest query features available in the database. Upon entering a KOG ID, the database is searched and if more than one gene maps to the same KOG ID, the out put page shows the list of genes in a table format. There may be instances where the output page contains same gene mapped to same KOG ID and the list appears redundant. This happens when the same KOG ID is part of multiple metabolic pathways. e.g; Upon searching for K08269 in Albugo laibachiiNC14 (V1), two records appear identical. This is because the KO ID linked to two different pathways e.g; one connects tomTOR signalling pathway with pathway id ko04150 and the other connects to regulation of autophagy pathway (pathway id ko04140). One another interesting feature in the output pathway map is the presence of boxes with red colored texts representing KOG IDs. This indicates the query organism also has curated proteins having KOG IDS that are part of the particular pathway.

Search for cluster ID/Group ID

    Enter Cluster ID :  
Input: Cluster Id/Group ID. e.g: 179
The cluster or the group ids are the group IDs generated by the clustering algorithm. We used OrthoMCL for clustering the protein sequences of 12 representative members e.g; Albugo laibachii Nc14, Phytophthora sojae (V5.0), Phytophthora ramorum Pr102, Phytophthora infestans T30-4, Phytophthora capsici LT1534, Phytophthora parasitica INRA-310, Hyalopernospora arabidopsidis Emoy2, Plasmopara halstedii, Pythium vexans DAOMBR484, Pythium ultimum DAOMBR144 (V1), Saprolegnia parasitica CBS223.65 (V1), Aphanomyces invadans. Conventionally the group with the largest number of proteins is Group 1 and the numbers of members are sorted in descending order.

Search by cluster description

    Enter Cluster description :  
Each of the clusters have a COG ID assigned to them post orthoMCL run. A key word search by the annotation based on the COGs will be able to pull out the cluster and its members when queried upon.
Input:example: condensin complex

Quick Search for Protein Domain/motif/function

    Select an organism :
      1. Albugo laibachii Nc14 (V1)
      1. Phytophthora agathidicida (V1)
      2. Phytophthora capsici LT1534 (V1)
      3. Phytophthora cinnamomi (V1)
      4. Phytophthora infestans T30-4 (V1)
      5. Phytophthora kernoviae (V1)
      6. Phytophthora multivora (V1)
      7. Phytophthora parasitica INRA-310 (V1)
      8. Phytophthora pluvialis (V1)
      9. Phytophthora ramorum (V1.1)
      10. Phytophthora sojae (V1)
      11. Phytophthora sojae (V5)
      12. Phytophthora taxon totara (V1)
      1. Plasmopara halstedii (V1)
      1. Pythium vexans DAOMBR484 (V1)
      1. Hyaloperonospora arabidopsidis Emoy2 (V8.3)
      1. Pythium aphanidermatum DAOMBR444 (V1)
      2. Pythium arrhenomanes ATCC12531 (V1)
      3. Pythium irregulare DAOMBR486 (V1)
      4. Pythium iwayamai DAOMBR242034 (V1)
      5. Pythium ultimum var.sporangiiferumBR650 (V1)
      6. Pythium ultimum DAOMBR144 (V1)
      1. Saprolegnia diclina VS20 (V1)
      2. Saprolegnia parasitica CBS223.65 (V1)
      1. Aphanomyces astaci (V1)
      2. Aphanomyces invadans (V1)


    Enter Protein Domain/motif/function :  
Search for Protein domain/motif/function curated from Interproscan Analysis
Example: tRNA-binding

Browse for SECRETOME/PROP/PSORT/SignalP/TMHMM

    Select an organism :

    Select output  
Secretome server predicts leaderless signal peptides and this is a feature based method contrary to signalP. SignalP on the otherhand, is a popular protein secretion prediction program based on leader sequences. In addition, there are several other prediction methods that helps understand the proteins better such as PROP, PSORT, TMHMM. PROP (predicts pro-protein cleavage sites at arginine and lysine residues (PMID: 14985543) using neural network. TMHMM predicts transmembrane regions of a protein and PSORT predicts sub-cellular localization of a protein. The parsed curated data of all the softwares mentioned above are available for download using this query option.
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