Biology Reference
In-Depth Information
Fig. 6 PRALINE server output page header
available to the user are PAM250 [
13
], BLOSUM62 and BLO-
SUM50 [
12
], and GON120 and GON250 [
46
].
Once a job is submitted to the PRALINE server, the user is
presented with a holding page that refreshes automatically. This
holding page shows which alignment steps are being performed by
the PRALINE server. Due to longer running times needed for
certain alignment strategies (e.g., homology-extended alignment),
the PRALINE server also provides the user with the possibility to
get an e-mail notification once the job is finished; this notification
e-mail contains a link to the outputs and some alignment statistics.
The output page presents general information about the align-
ment (alignment score, alignment length, number of gaps, etc.)
(Fig.
6
). It also contains information such as PSI-BLAST output,
secondary structure predictions, or TM predictions depending on
the alignment strategy selected by the user. On this page the user
can also select various predefined color schemes to visualize the
alignment according to residue type, hydrophobicity, secondary
structure (if applicable), or TM structure (if applicable). Each
color scheme comes with a concise explanation as to how to inter-
pret the different colors. Apart from the predefined color schemes,
the users can also define their own color scheme using a custom
