mapp2g

Mapp2g

Installation

Pre-requisites

• NCBI blast
• exonerate

These two software should be installed. mapp2g is wrtten in Ruby. Ruby sholud be installed.

Install mapp2g using gem

gem install mapp2g

Usage

Usage: mapp2g [options]
    -q, --query QUERY                query amino acid sequences in FASTA format
    -g, --genome BLASTDB             genome reference as blastdb
    -o, --outdir [OUTDIR]            output directory. DEFAULT: mapp2g_out_{process_id}
    -v, --version                    show version number
    -h, --help                       show this help message and exit

Query sequences should be in FASTA format. Multiple sequences can be included in one file.

(example)

mapp2g -q human_genome.fasta -q p53.protein.fasta

Reference genomes should be formated in blastdb before running mapp2g. blastdb can be made as follws:

makeblastdb -in human_genome.fasta -dbtype nucl -parse_seqids

Outputs

For each query, the following files are generated.

• query sequence in fasta
• blast output in tab-delmited format (format 6)
• exonerate full output
• exonerate alignment in gff3 format
• report.json

report.json contains all of the information above in json line format.

License

The gem is available as open source under the terms of the MIT License.