The Lotus japonicus Genome

is known. Partial sequence of genomic DNA

is not recommended since the program may

notfind a sequence from an intron. There are

two options for target database in the drop

down menu, the Affymetrix probe target

sequence (the whole transcript) and the Af-

fymetrix probe consensus sequence (the parts

of the transcript to which the probe sets bind).

Users of the BLAST search option should

always check the alignment (which comes as

an additional output, Fig.17.2) to be sure that

the given transcript really corresponds to the

sequence of interest.

17.4.2 The Result Output Page

There are several layers of result output

(Fig.17.3). Thefirst layer gives the corresponding

probe set ID and the values of transcript abun-

dance. There is a clickable button, which will

provide the graphic representation of the transcript

level in all the tissues tested. Users can download

batch results in the case of multiple queries or more

generalized queries such as GO or gene descrip-

tion. There is also an‘add to transcript viewer’

feature that helps to view multiple transcripts on

the same graph so that users can compare between

Fig. 17.2 Using the BLAST option: A nucleotide
sequence can be used as a search query in the BLAST
option. The result page comes with an additional link,
which will open the alignment (inseton thelower right).

The bases aligned are marked in green. The individual

probes are indicated by alternativeredandbluecolors,

while the overlapping portions between two consecutive

probes areunderlined

17 A Tutorial onLotus japonicusTranscriptomic Tools 193