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  • Published: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

Published: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

Access article:

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z

Comments

  • EagleEye 188 days ago
     
     

    Gene Set Clustering based on Functional annotation (GeneSCF)

    ---------------------- 13/01/2017 ---------------------------

    Due to recent changes (naming convention in FTP files) from the database KEGG (01/January/2017) and Gene Ontology (January 2017), the GeneSCF (v1.1 and v1.1-p1) file retrieval utility was unsuccessful with following issues when using update mode (--mode=update),

    Example of reported issue: https://www.biostars.org/p/231071/

    Other possible issues:

    • Creating empty output files

    • Less number of genes mapping to KEGG when using GeneSymbol as input

    • Some organism from Gene Ontology was not supported

    The above mentioned issues was faced by GeneSCF v1.1, v1.1-p1 users from 01/January/2017. All the problems are now rectified with new patch release GeneSCF v1.1-p2 (13/January/2017).

    ---------------------- 13/01/2017 ---------------------------

    Download: http://genescf.kandurilab.org/downloads.php

    Thanks to all users for supporting GeneSCF and please report if there is any problem. We will continue to work on GeneSCF improvements by considering users feedback.

    **

    Note: Please always use new (updated) version of GeneSCF.

    **

  • EagleEye 168 days ago

    --------------------- 09/02/2017 ---------------------------

    GeneSCF v1.1 (patch release 2) News : All features are successfully tested on Microsoft Windows 10 bash (version 1607)

    • required installation of 'unzip' utility on windows bash using 'sudo apt-get install unzip'
  • Marysia 162 days ago

    Thanks for GeneSCF, it is really useful. 

    I am dealing with new genome, with priliminary annotations. The annotated ids are not universally accepted. Once I tried to convert the ids/sequence by matching online database, it fail as most of them does not have significant hits !! Is thare any way to check gene enrichments study for new genomes? Is there any posibility to update your tools for the same?

    Note:I guess BLAST2GO could help, but it is paid version :(

  • EagleEye 161 days ago

    First of all thanks for using GeneSCF.

    I am really sorry to say that current GeneSCF does not support new genome annotation. Since many users are requesting, it is possible that we may include this feature in new release along with other improvements (we will try our best to release a early as possible). 

    Suggestion: Do you have any closest species/organism/strain ? If so try this,

    1) Get best matching geneids for individual genes from blastn

    > blastn -query gene1.fa -out gene1.blast.txt -task megablast -db closest_species -evalue 1e-10 -best_hit_score_edge 0.05 -best_hit_overhang 0.25 -outfmt 7 -perc_identity 50 -max_target_seqs 1

    2) Use those geneids/symbols in GeneSCF.

     

  • Abhimanyu Singh 85 days ago

    Thanks for developing geneSCF, I tried to install it but got the following error

    bio@bio214b[geneSCF-master-source-v1.1-p2] ./prepare_database []

    prepare_database USAGE:

    ./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -org=[see,org_codes_help]

    ==========
    Options: ALL PARAMETERS MUST BE SPECIFIED
    ==========

    [-db= | --database=] Options:[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME]

    [-org= | --organism=] Options:[see,org_codes_help]

     

    bio@bio214b[geneSCF-master-source-v1.1-p2] ./prepare_database -db GO_all -org see []
    Error:Please specify one of these databses GO_all,GO_BP,GO_MF,GO_CC,KEGG,NCG,REACTOME

     

  • Abhimanyu Singh 84 days ago

    Thanks, I will have a look.