Hi Jean, > Does any program in EMBOSS package can make use of the Reference Sequence > Databases? I indexed refseq databases with dbxflat and run showfeat against > them but receive error about has zero length sequence :
The next release will include refseq as a valid sequence format. You can usually get away with defining the format as Genbank. If that does not work please let me know and I will update the refseq format code. Aha ... but in this case ... NG_002612 does have zero length. This appears to be one of those entries (the EMBL CON division does much the same) that only refer to sequence data in other entries. It ends with the line: CONTIG join(complement(AC006998.3:2483..110100)) We can try to process these. The database defintion will need to know where to look up "AC006998.3" which is where the sequence data ... and all the missing features ... should be. Can you exclude the CON entries from your indexing? if not, we can try excluding them. Hope that helps, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
