[EMBOSS] strange frames

[Stefan Rensing]

Dear all,

apparently, sixpack/transeq handle frames on the reverse complementary
strand different than e.g. BLAST does (and different than I would have
expected).

Using sixpack/transeq to translate this sequence:

AGATGACTCCGTTGCAGTTGGCTACTGCTTATATTGCATCAGGGGGTGTGCTTCA

Sixpack output:

       R  *  L  R  C  S  W  L  L  L  I  L  H  Q  G  V  C  F  X        F1
        D  D  S  V  A  V  G  Y  C  L  Y  C  I  R  G  C  A  S          F2
         M  T  P  L  Q  L  A  T  A  Y  I  A  S  G  G  V  L            F3
     1 AGATGACTCCGTTGCAGTTGGCTACTGCTTATATTGCATCAGGGGGTGTGCTTCA      55
       ----:----|----:----|----:----|----:----|----:----|----:----|
     1 TCTACTGAGGCAACGTCAACCGATGACGAATATAACGTAGTCCCCCACACGAAGT      55
        L  H  S  R  Q  L  Q  S  S  S  I  N  C  *  P  T  H  K          F6
       X  I  V  G  N  C  N  A  V  A  *  I  A  D  P  P  T  S  *        F5
         S  S  E  T  A  T  P  *  Q  K  Y  Q  M  L  P  H  A  E         F4

Transeq output:

Frame -2:
>>test_4
EAHPLMQYKQ*PTATESS

Frame -1:
>>test_5
*STPPDAI*AVANCNGVIX

Frame -3:
>>test_6
KHTP*CNISSSQLQRSHL

IMHO, it should be:
Frame 1 = +1
Frame 2 = +2
Frame 3 = +3
Frame 4 = -1
Frame 5 = -2
Frame 6 = -3

However, in this case, sixpack and transeq return:
Frame 1 = +1
Frame 2 = +2
Frame 3 = +3
Frame 4 = -2
Frame 5 = -1
Frame 6 = -3

Is this the expected behaviour, and if so, why?

Regards,

Stefan


-- 
Dr. Stefan Rensing, Group Leader Computational Biology
Plant Biotechnology, Faculty of Biology, University of Freiburg
Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
http://www.plant-biotech.net/  http://www.cosmoss.org/
stefan.rensing at biologie.uni-freiburg.de

"Mr. Musgrave, please don't interrupt me when I'm asking rhetorical
questions."