This is a valuable way to
establish relationships and compare the relationships between multiple protein
sequences. One valuable application is
phylogentics, where the degree of sequence homology between proteins can be
used to determine the relationships between species.
For information pertaining
to Clustal W version 1.8 refer to:
ClustalW 1.8 Online Help File at Baylor College of Medicine
Instructions:
1. The sequences to be test must be obtained and the form in
which they are pasted into the box is important. Also, each sequence must be
pasted into the box in the same format.
2. Click on the “Most ReadSeq formats accepted” hyperlink to
check acceptable input formats. You will find for many of these types of
applications that the FASTA format is the easiest to Copy and Paste with.
3. We suggest using the FASTA format that can be accessed
via the following pathway, see Protein Sequence Retrieval directions for
instructions on how to obtain FASTA sequence information.
4. Under “choose alignment method”, we suggest using “PIMA
1.4.” (however, each of the methods has beneficial aspects and is worth
experimenting with).
5. Paste sequences into the box in the following manner. In
the first line, type in a greater-than character (‘>’) followed by a comment
or title for the sequence. Press enter to start a new line. This second line
should contain the sequence.
6. Copy (Ctrl + C) your sequence in some acceptable format.
7. Paste (Ctrl + V) that sequence into the line following
the greater-than character (‘>’). You may also type in the sequence by hand.
8. Repeat steps 5-7 until desired number of sequences is
entered into the box. Each sequence must be pasted by this method.
9. Click on the “Submit” button to start the program.
Note: For each
new sequence entry, you must type in a greater-than character (‘>’) to
inform the program that the entry is a different sequence from the previous.
The following sequence input was for FASTA format.
10. The results will be returned with sequences listed on
top of each other after efforts have been made for alignment. The first sequence
listed is the programs attempt to find the conserved sequence. If an amino acid
is conserved throughout the sequence, it will be listed. However, the program
also matches pays attention to amino acid classes, that are a result of side
chain similarities. (see the Amino Acid Classes description below).
Amino Acid Classes Match score -2 _______________ X __________________ 0 / / \ \ _ f _ / ______r _______ \ 1 / / \ / / / \ \ \ / c \ e / m p \ _ j __ 2 / / \ \ / \ / / \ / \ \ / \ \ / a b d \ / l k o n i h \ 3 / / \ / \ /|\ \ / / \ / \ / \ /\ / \ / \ \ C I V L M F W Y H N D E Q K R S T A G P 5
If you need more assistance, please refer to the Help
section of the program.
When you are ready, click
here to start.
Baylor
College of Medicine (BCM) Search Launcher: Multiple Alignments.