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• • EagleEye@santhilalsubhash

  

  EagleEye 2863 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@santhilalsubhash

  

  EagleEye 2844 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@marysia

  

  Marysia 2837 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@santhilalsubhash

  

  EagleEye 2837 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@abhimanyu

  

  Abhimanyu Singh 2761 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

   

• • EagleEye@santhilalsubhash

  

  EagleEye 2761 days ago

  Please check the documentation (no installation is needed, extract and use),

  https://www.biostars.org/p/231384/#231579

  https://www.biostars.org/p/108669/

  http://genescf.kandurilab.org/documentation.php

• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh 2760 days ago

  Thanks, I will have a look.