Once gene sequences have been identified in the genome, it is possible to use sequence alignment programs (such as FASTA or BLAST) to detect matching regions in the nucleotide sequence. These matching regions are potential gene homologs and are termed pseudogenes if there is some evidence that either of the causes (see above) are satisfied.
In these analyses, genes from annotated genomes and protein databases have first been clustered into paralog families and then used to survey whole genomes for copies or homologs. For each potential pseudogene (or fragment) match, a number of steps have been taken to assess its validity as a pseudogene.
These steps include checking for overcounting and repeat elements, overlap on the genomic DNA with other homologs and cross-referencing with exon assignments from genome annotations. The resulting pseudogenes or pseudogenic fragments have then been assigned to the paralog family of the most homologous gene (or assigned to a singleton gene if the probe gene has no obvious paralog).