PreparingOMA

Preparing OMA files

When working with orthologs from the OMA database, 2 files have to be downloaded from OMA database – OMA groups (http://omabrowser.org/All/oma-groups.txt.gz) and OMA Protein Sequences (http://omabrowser.org/All/oma-seqs.fa.gz). If you don't want to use the create_conf.pl script for downloading the data, perform the following steps:

Always check for the latest versions at http://omabrowser.org/oma/current/. Once downloaded, do the following:

• unzip the oma groups file

gunzip oma-groups.txt.gz

• unzip the fasta file

gunzip oma-seqs.fa.gz

• Convert Multi-line fasta to single-line fasta

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END
{printf("\n");}' < oma-seqs.fa > oma-seqs.fa

• remove white spaces in the fasta headers

sed –i –e ‘s/> />/’ oma-seqs.fa

Now, the OMA files are ready to be used with protTrace. Provide the path of these files in the program configuration file under tabs path_oma_group and path_oma_seqs respectively.