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functional_annotation's Introduction

Functional_Annotation

Scripts to functionally annotate genes

Databases needed:

  1. SwissProt (mmseq2 database formatted)
  2. TrEMBL (mmseq2 database formatted)
  3. PFAM_A
  4. KOFAM

Programs needed:

  1. mmseq2 (https://github.com/soedinglab/MMseqs2)
  2. pfam_scan.pl (http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz)
  3. HMMER-3.1b2 (http://eddylab.org/software/hmmer/hmmer-3.1b2.tar.gz)
  4. kofamscan (https://github.com/takaram/kofam_scan)

To run annotation:

  1. Copy control script run_FuncAnnot_MMseqs.sh into your working directory
  2. Change the specified variables within the script to those that are appropriate for your system (e.g. path to mmseq2, hmmer, etc.)
  3. Run the script ./run_FuncAnnot_MMseqs.sh to start the functional annotation process

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