GenMine

A GenBank data mining program for (mostly fungal) taxonomists

GenMine downloads GenBank nucleotide records GenMine filters downloaded data with frequently used genes in taxonomy.

Citation: Chang Wan Seo, Sung Hyun Kim, Young Woon Lim & Myung Soo Park (2022) Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine, Mycobiology, DOI: 10.1080/12298093.2022.2116816

https://www.tandfonline.com/doi/full/10.1080/12298093.2022.2116816

Installation

• pip

pip install GenMine

• conda

conda install -c cwseo GenMine

Usage

Basic usage

• Download all Penicillium records

GenMine -e wan101010@snu.ac.kr -g Penicillium

• Download all Penicillium records and then filter records with term "Korea"

GenMine -e wan101010@snu.ac.kr -g Penicillium -a Korea

• Download data accession numbers

GenMine -e wan101010@snu.ac.kr -c ON417149.1 ON417150.1

Advanced usage

• Download records of multiple genera

GenMine -e wan101010@snu.ac.kr -g Penicillium Trichoderma Alternaria

• Download records of multiple genera given by file

GenMine -e wan101010@snu.ac.kr -g genera.txt

"genera.txt" should be like this

Penicillium
Trichoderma
Alternaria

• Download records of multiple accession given by file

GenMine -e wan101010@snu.ac.kr -c accessions.txt

"accessions.txt" should be like this

ON417149.1
ON417150.1
MW554209.1
OK643788.1

• Continue download from interrupted run (only for accessions, for genus, it will automatically solve if you launch GenMine in same location)

GenMine -e wan101010@snu.ac.kr -c accessions.txt -o "2022-11-02-00-12-08"
# Caution 1: -o should be name of previous run result directory
# Caution 2: will not work for finished run

Arguments

• Basic Parameters

--genus, -g : List of genus to find | File with genera in each line
--accession, -c : List of accessions to get | File with accessions in each line
--email, -e : your email for NCBI access

• Optional Parameters

--additional, -a : additional terms (ex. country name) to filter 
--max, -m : maximum length of the sequence to parse (default: 5000)

Output explanations

Main output

WIP

Features

GenMine is a python program that parses records from GenBank and sort by gene names, based on Entrez library. Comparing to Entrez, GenMiner has some advantages and disadvantages

Advantages

• GenMine doesn't misses records, especially with multiple terms
• GenMine can download discontinuously, especially useful in low internet condition
• GenMine classifies downloaded records by gene types (ITS, LSU, SSU, BenA etc...)

• If you want more gene types, issue it!
• We are currently working on better gene annotations

Limitations

• Slower than Entrez (sometimes a lot), due to completeness and stability

Bug reports and Suggestions

• Bug reports and suggestions are available in Github Issues or directly to wan101010@snu.ac.kr
• However, we want GenMine to remain as small tool. For suggestions little bit too much for the purpose of GenMine might be accepted in our upcomming softwares