Findorf 2003 version 1.0 and Transfasta 2003 version 1.0 have been programmed using Perl language, executable from Linux. Web sites have been done by using HTML language.

Herpes viruses sequences have been obtained from GeneBank in the NCBI page11 (table 1).


Table 1:

HerpesvirusStrainAccession number
EHV-1Ab4pM86664
EHV-4NS80567AF030027


To predict possible orfs in that genomes we have firstly transformed herpesvirus sequences to fasta format using Transfasta 2003 version 1.0 (see EHV1fasta, EHV4fasta). Afterwards, we have submit the sequences to Orfinder 2003 version 1.0 considering the conditions in table 2. Minimum lenght of 100 aminoacid has been chosen because of the high probability of random results in shorter sequences6.


Table 2:

Findorf 2003 version 1.0 considered conditions
Minimum lenght100 aa
Searching in complementary chainyes
Starting with Metyes


Identification of predicted orfs by Findorf 2003 version 1.0 yet annotated has been done by comparison with annotations in equine herpesvirus 1 and 4 sequences in GeneBank11 and with Telford et al. 19982. Non-identifyed orfs have been submited to PSI- and PHI-Blast11 to find possible identities with other genes in the databank.

Finally, orf providing blast results with E value better than threshold (0.005) have been aligned with the new sequences using Clustalw7 to check the results: if they are significative they will show good alignment with the predicted orf.