Clustal W multi sequence alignment with secondary structure constraints

Question

[JJP]

Hello,

I am trying to align multiple sequences using constraints on secondary structure of one of the structures. Here are the sequences with secondary structures for one of them:

seq1:

NLLPYFDFDVPRNLTVTVGQTGFLHCRVERL
GDKDVSWIRKRDLHILTAGGTTYTSDQRFQVLRPDGSANWTLQIKYPQPRDSGVYECQINTEPKMSLSYTF

seq1-SS:

!SS_Dpr1 
....aaaAAAAAaaaaAAAAAAAAAaaaaAAAAAAaaaAAAAAAaaAAAaaaaaAAAAaaa..aaaAAAAaaa..aaaAAAAAAAaaa.aaaAAAAA

seq2:

WMEPYFDPSTP
RNVTALMGKSAYLSCRVRNLANKTVSWIRHRDIHILTVGSYTYTSDQRFQATHHQDTEDWTLQIKWAQKRDAGMYECQIS
TQPVRSYFVRL

Here, seq1-SS denotes the cost of breaking different regions of the secondary structure.

I am using the "Profile Alignment Mode" to input the two sequences and one of the secondary structure.

Here are my questions:

1. When I combine the secondary structure and sequence information for seq1 in one file, Clustal W does not output the correct total number of sequences. Rather, it adds the two lines (total number of sequences in the file and their corresponding secondary structure codes). Obviously, that is wrong. How do I fix it?

2. I have tried importing the sequence and secondary structure information for seq1 separately but I don't think it reads the information correctly.

If anyone could guide me how to import the two "profiles" including one of the secondary structure information to perform multi-sequence alignment, that would be really helpful.

Thank you in advance for your time and help with this! I appreciate your time.

Best,
JJP

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.