Can I use NCBI databases with GrailEXP?
Yes, as long as you index them and formatdb them. NCBI headers also maintain the accession number in the second field. However, the program will not be able to get organism or database tag information out of the header. The database tag (3rd field) is not used by the program; it is merely returned to the user in the alignment output file. NCBI has a data source tag in the 3rd field (dbj, emb, gb, etc.), so this works out all right. The only remaining problem is the first field, which is expected to contain organism information by Gawain (the gene assembly program). However, the only way in which this information is used is to weight matching alignments higher in building gene models. This can be important, as mouse alignments can sometimes create noise that mess up the human gene models. The way to solve this problem is to maintain human, mouse, etc. in separate databases, so that distinguishing between organisms never becomes an issue. So the two options are to use NCBI-header databas
