Tag Sequence for 454 data

[Mona]

hi, m trying to perform de novo assembly with Mira on data coming from 454.
in the Mira manual it is written to screen the sequences for the tag sequences, that we should know already before starting the assembly. Can anybody please tell me, what is the tag sequence in case of 454 sequnces coming from FLX. and also if this tag sequence is used only for pair end reads or for single end reads also.

[flxlex]

Usually, there will be no tag on 454 reads. Unless your sequence provider has added MID tags on the samples during library prep, in which case they should have removed them before giving you the reads (you could ask them). With paire ends, there is not really a 'tag', but a linker sequence. I would check the mira manual on how it copes with 454 paired ends (I vaguely remember having heard/read that you have to pre-process the reads to get rid of the linker and /or split the reads in halves).

[Mona]

ok.. thnx
it means while running de novo assembly on Mira, i only have to provide the fasta file containg reads, fasta quality files and XML trace info file. and no need to screen the data before running it on mira.