Biology Reference
In-Depth Information
Fig. 3 Comparison of R-Coffee and T-Coffee RNA alignments. The color code indicates the type of com-
plementarities between matching columns. Orange columns marked with a “W” correspond to perfect
Watson-Crick (WC) pairing, without mutation. Green columns marked with an “N” are columns containing
either WC or GU pairs (neutral). Blue columns marked with a “T” indicate position containing non-WC pairs.
Red columns correspond to perfect WC positions, including compensated mutations, marked with a “C”
The current versionof Pro-Coffee uses a default gap-opening
penalty (GOP) of
1.
Yet, our benchmarks suggest that good promoter alignmentsmay
be obtained using GOP values between
60 and a gap-extension penalty (GEP) of
70 while
keeping the GEP at the default value. To show how alternative
values can be explored, here we give the command line that
explicitly spells out the default parameters:
t_coffee
50 and
-seq
<
your
seq
>
-method promo_pair@EP@
GOP@-60@GEP@-1
2. RNA sequences: R-Coffee
R-Coffee [
16
] is a special mode of T-Coffee for aligning
noncoding RNAs with conserved secondary structures
(the predicted secondary structures are generated as output
files rfold_files). This mode can also be used to analyze com-
pensated mutations in the resulting MSA using a homemade
reference benchmark from DARTS, a database of RNA
sequences with known 3D structure. R-Coffee (Fig.
3
)isrun
using the following command:
t_coffee
-seq RNA_rcoffee.fa
-mode
rcoffee
-outfile
RNA_rcoffee.aln
One of the main advantages of noncoding RNA in
sequence analysis is the relative clear pattern left by compen-
sated mutations when doing multiple sequence analysis. Given
an RNA alignment with either a predicted or an estimated
secondary structure, the seq_reformat option of T-Coffee can
be used to estimate the number of columns showing compen-
sated mutations by the following command:
t_coffee -other_pg seq_reformat -in RNA_rcoffee.aln
-action +alifold2analyze color_html
>
RNA_tcoffee.html
