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Create-Marker-Gene-Database

Scripts for creating "marker gene" reference files for use as database for sequence similarity searches

Overview

The generate_annotation.sh is taking a FASTA file with common header format as can be usually found in UniProt, NCBI, etc. and performs the following:

  • Dereplicate sequences by 97 percent similarity with cd-hit
  • Convert FASTA to one-line format and remove header description (after whitespace) with awk
  • Convert headers to md5 with python script convert_fasta_headers_md5.py
  • Merge files to create a complete annotation file with python script merge_annotation_files.py

Software requirements

cd-hit
Pandas (Python)

Requred files

  • FASTA file (.fa extention)
  • Tab-seperate annotation file (same name as FASTA with .tab exention)

Downloaded from UniProt, for example:
https://www.uniprot.org/uniprot/?query=terminase+family%3Aprotein+taxonomy%3A%22Viruses+%5B10239%5D%22&sort=score

Output files

  1. derep.fa
  2. derep.md5.fa
  3. derep.fa.clstr
  4. annotation.tsv