EuGene annotation transfer
egn_annotation_transfer.pl makes possible to transfer the structural annotation of a sequence onto another sequence.
There is no gene discovery, only the genes of the initial annotation are transferred to the new sequence.
The genes annotated on the new sequence will have a "valid" structure, one that is compatible with EuGene’s internal gene model (e.g. every CDS starts with a start codon, ends with a stop codon, and has a length which is a multiple of three).
The name of the source gene is indicated in the "Alias" attribute of the output GFF3 file.
The program is useful to transfer the annotation between genotypes/strains of the same species while preserving the correspondence between genes.
Notes:
-Only genes that code for a protein are transferred.
-The default configuration is suitable for eukaryotic genomes.
Advice:
- To improve sensitivity of the transfer, make sure SIBsim4 is in the path (SIBsim4 is available as a debian package).
Usage:
The genes annotated on the new sequence will have a "valid" structure, one that is compatible with EuGene’s internal gene model (e.g. every CDS starts with a start codon, ends with a stop codon, and has a length which is a multiple of three).
The name of the source gene is indicated in the "Alias" attribute of the output GFF3 file.
The program is useful to transfer the annotation between genotypes/strains of the same species while preserving the correspondence between genes.
Notes:
-Only genes that code for a protein are transferred.
-The default configuration is suitable for eukaryotic genomes.
Advice:
- To improve sensitivity of the transfer, make sure SIBsim4 is in the path (SIBsim4 is available as a debian package).
Usage:
% export EGNEP /path/of/eugene/pipeline % export EUGENEDIR /path/of/c++/eugene/software % $EGNEP/bin/int/misc/egn_annotation_transfer.pl --scaffolds multifasta file Genomic sequence to annotate --ref_scaffolds multifasta file Genomic sequence of reference --ref_gff3 GFF3 file Reference annotation --outfile GFF3 file Result annotation (must end with .gff3) --workingdir directory Working directory --cfg file Configuration file. Example: $EGNEP/cfg/egn_annotation_transfer.cfg
