Query: Multiple Sequence Alignment - (Jul/09/2008 )
Hi, I always use the NCBI tool just go to BLAST and then click aligment two sequences, that program identify if the sequences have two match sites. Remember if you sent the sample to sequencing with forward and reverse primers one of the results is given in the oposite direction and you have to use the reverse complement, if you don't do that you can not have a real aligment.
Good luck
-u01dfd7-
QUOTE (u01dfd7 @ Jul 11 2008, 07:44 AM)
Hi, I always use the NCBI tool just go to BLAST and then click aligment two sequences, that program identify if the sequences have two match sites. Remember if you sent the sample to sequencing with forward and reverse primers one of the results is given in the oposite direction and you have to use the reverse complement, if you don't do that you can not have a real aligment.
Good luck
Good luck
hi. I did use BLAST2seq at NCBI to find the final consensus seq. thanks
-dsain-
QUOTE (dsain @ Jul 11 2008, 10:27 AM)
QUOTE (u01dfd7 @ Jul 11 2008, 07:44 AM)
Hi, I always use the NCBI tool just go to BLAST and then click aligment two sequences, that program identify if the sequences have two match sites. Remember if you sent the sample to sequencing with forward and reverse primers one of the results is given in the oposite direction and you have to use the reverse complement, if you don't do that you can not have a real aligment.
Good luck
Good luck
hi. I did use BLAST2seq at NCBI to find the final consensus seq. thanks
For multiple aligment, you should use a minimum of 5 sequences, if it is a pairwise alignment, then y did u choose Clustal W, Strap and T-coffee.???
-Biorad-
QUOTE (Biorad @ Jul 15 2008, 09:18 PM)
QUOTE (dsain @ Jul 11 2008, 10:27 AM)
QUOTE (u01dfd7 @ Jul 11 2008, 07:44 AM)
Hi, I always use the NCBI tool just go to BLAST and then click aligment two sequences, that program identify if the sequences have two match sites. Remember if you sent the sample to sequencing with forward and reverse primers one of the results is given in the oposite direction and you have to use the reverse complement, if you don't do that you can not have a real aligment.
Good luck
Good luck
hi. I did use BLAST2seq at NCBI to find the final consensus seq. thanks
For multiple aligment, you should use a minimum of 5 sequences, if it is a pairwise alignment, then y did u choose Clustal W, Strap and T-coffee.???
I used Strap and T coffee for doin MSA of 9 protiens and then found out the consensus of the MSA for both the programs. But to reconcile the alignments, I had to find a single consensus sequence..which I tried to do by blasting the 2 cons seq with each other using Blast2seq.
dsain
-dsain-
QUOTE (dsain @ Jul 16 2008, 01:53 PM)
I used Strap and T coffee for doin MSA of 9 protiens and then found out the consensus of the MSA for both the programs. But to reconcile the alignments, I had to find a single consensus sequence..which I tried to do by blasting the 2 cons seq with each other using Blast2seq.
dsain
dsain
May be Vadlo will point you to at least a dozen different algorithm if not more. Check for protein ones.
http://search.vadlo.com/b/q?sn=158621799&a...nment&rel=1
Let us know if any two give the same results
-cellcounter-