next up previous
Next: output type Up: OPTIONS Previous: input type

alignment on protein level for DNA sequences

option: -T [translation]
default: alignment computed on DNA level
usage: dialign-t -T <conf-dir> <input-file> [output-file]
WARNING: Do not use -D in this case although it is DNA input!

DNA sequences will be translated into aminoacids. The length of the sequences will be cut to mod 3 = 0. The aminoacids will be aligned and then retranslated into DNA sequences for output.

option: -O [with ORF finder]
default: alignment computed on DNA level
usage: dialign-t -O <conf-dir> <input-file> [output-file]
WARNING: Do not use -D in this case although it is DNA input!

DNA sequences will be translated into aminoacids. The reading frame for each sequence is calculated due to its Longest Open Reading Frame. The aminoacids will be aligned and then retranslated into DNA sequences for output.

option: -L [only ORF]
default: alignment computed on DNA level
usage: dialign-t -L <conf-dir> <input-file> [output-file]
WARNING: Do not use -D in this case although it is DNA input!

DNA sequences will be translated into aminoacids. Only the Longest Open Reading Frame of each sequence will be aligned. Retranslation into DNA Sequences for output.


next up previous
Next: output type Up: OPTIONS Previous: input type
Volker Menrad 2005-03-25