Why do I get protein sequences that are shorter than orfminsize/3 when I use that option with sixpack? Do I misunderstand what an ORF is?
ebs15242@biox:~/Data/EMBOSS$ sixpack -orfminsize 500 kras.gb Display a DNA sequence with 6-frame translation and ORFs Output file [nm_004985.sixpack]: protein output sequence(s) [nm_004985.fasta]: ebs15242@biox:~/Data/EMBOSS$ head nm_004985.fasta >NM_004985_1_ORF1 Translation of NM_004985 in frame 1, ORF 1, threshold 500, >62aa GRGGGGSSGGGSGGGEGGGGSASTPGPRHFGLGASAAQALKAAAGPEAQRLPGAGERPAE ND >NM_004985_1_ORF2 Translation of NM_004985 in frame 1, ORF 2, threshold 500, >31aa SKICNIFVMNCTTPNYCNVIKIVTVTKKKKX 62aa and 31aa lead to sizes of 186bp and 93bp. What's happening to the other 300-400 base pairs in the ORF? Why are they not getting translated? _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss