po2anno

po2anno

po2anno.pl is a script to create an annotation comparison matrix from Proteinortho5 output.

• Synopsis
• Description
• Usage
  • cds_extractor
  • Proteinortho5
  • po2anno
• Options
  • Mandatory options
  • Optional options
• Output
• Run environment
• Author - contact
• Changelog

Synopsis

perl po2anno.pl -i matrix.proteinortho -g genome_fasta_dir/ -l -a > annotation_comparison.tab

Description

Supplement an ortholog/paralog output matrix from a Proteinortho5 calculation with annotation information. The resulting tab-separated annotation comparison matrix (ACM) is mainly intended for the transfer of high quality annotations from reference genomes to homologs (orthologs and co-orthologs/paralogs) in a query genome (e.g. in conjunction with tbl2tab.pl). But of course it can also be used to have a quick glance at the annotation of genes present only in a couple of input genomes in comparison to the others.

Annotation is retrieved from multi-FASTA files created with cds_extractor.pl. See cds_extractor.pl for a description of the format. These files are used as input for the PO analysis.

Proteinortho5 (PO) has to be run with option -singles to include also genes without orthologs, so-called singletons/ORFans, for each genome in the PO matrix (see the PO manual). Additionally, option -selfblast is recommended to enhance paralog detection by PO.

Each orthologous group (OG) is listed in a row of the resulting ACM, the first column holds the OG numbers from the PO input matrix (i.e. line number minus one). The following columns specify the orthologous CDS for each input genome. For each CDS the ID, optionally the length in bp (option -l), gene, EC number(s), and product are shown depending on their presence in the CDS's annotation. The ID is in most cases the locus tag (see cds_extractor.pl). If several EC numbers exist for a single CDS they're separated by ';'. If an OG includes paralogs, i.e. co-orthologs from a single genome, these will be printed in the following row(s) without a new OG number in the first column. The order of paralogous CDSs within an OG is arbitrarily.

The OGs are sorted numerically via the query ID (see option -q). If option -a is set, the non-query OGs are appended to the output after the query OGs, sorted numerically via OG number.

Usage

cds_extractor

for i in *.[gbk|embl]; do perl cds_extractor.pl -i $i [-p|-n]; done
rename 's/_cds_[aa|nuc].fasta/.[faa|fna]/' *_cds_[aa|nuc].fasta

Proteinortho5

proteinortho5.pl -graph [-synteny] -cpus=# -selfblast -singles -identity=50 -cov=50 -blastParameters='-use_sw_tback' *.[faa|fna]

po2anno

perl po2anno.pl -i matrix.[proteinortho|poff] -g genome_fasta_dir/ -q query.[faa|fna] -l -a > annotation_comparison.tab

Options

Mandatory options

• -i, -input

  Proteinortho (PO) result matrix (*.proteinortho or *.poff), or piped STDIN (-)

• -g, -genome_dir

  Path to the directory including the genome multi-FASTA PO input files, created with cds_extractor.pl

Optional options

• -h, -help

  Help (perldoc POD)

• -q, -query

  Query genome (has to be identical to the string in the PO matrix) [default = first one in alphabetical order]

• -l, -length

  Include length of each CDS in bp

• -a, -all

  Append non-query orthologous groups (OGs) to the output

• -v, -version

  Print version number to STDERR

Output

• STDOUT

  The resulting ACM is printed to STDOUT. Redirect or pipe into another tool as needed (e.g. cut, grep, head, or tail).

Run environment

The Perl script runs under Windows and UNIX flavors.

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Changelog

• v0.2 (15.01.2015)
  • give number of query-specific OGs and total query singletons/ORFans in final stat output
  • changed final stat output to an easier readable format
  • fixed bug: %Query_ID_Seen included also non-query IDs, which luckily had no consequences
• v0.1 (18.12.2014)