Optimal Pairwise Alignment Tools - University of Missouri - Kansas ...

Step 3: Select appropriate “Gap Open” and “Gap Extend” penalties from their respective
drop-downs. EMBOSS provides only limited values, and it doesn’t have an option where
the user can specify values of their choice.
Step 4: Select molecule type “DNA”, if the purpose is to compare two DNA sequences,
or select molecule type as “Protein” to compare protein sequences. EMBOSS doesn’t
provide options to compare a DNA-protein sequence.
Step 3: Select appropriate Gap Open and Gap Extend penalties from their respective
drop-downs. EMBOSS provides only limited values, and it doesn’t have an option where
the user can specify values of their choice. Possible values for Gap Open are 1, 5, 10, 15,
20, 25, 50 or 100 with 10 being the default. Possible values for Gap Extend are 0.1, 0.2,
0.4, 0.5, 0.6, 0.8, 1, 5 and 10 where 0.5 is the default.
Step 4: Select molecule type as “DNA”, if the purpose is to compare two DNA
sequences, or select molecule type as “Protein” to compare protein sequences. EMBOSS
doesn’t provide options to compare a DNA-Protein sequence.
Step 5: Select a “Substitution Scoring Matrix” from the matrix drop-down. If the
selected molecule type is “Protein”, then select from a restricted range of PAM and
BLOSUM matrices. The choices are Blosum40, Blosum50, Blosum62, PAM50,
PAM100, and PAM250. The default selection is Blosum62. If the selected molecule is
“DNA”, then select either DNAmat or DNAfull.
Step 6: In order to compare two sequences, input two sequences in each of the text
windows. Sequences can be input either by typing or pasting the “free-text” sequence
which is simply a block of characters specifying either “DNA” or “Protein” sequence or
by even uploading the input sequences from a file format. EMBOSS allows the user to
input the sequences in many standard formats like GCG, FASTA, GENBANK etc.
Step 7: Verify all selected options and click on “Run” to view the results of global or
local alignment. Otherwise click on “Reset” in order to specify the options starting from
defaults.
Step 8: EMBOSS will align input sequences according to the chosen alignment, and will
specify the percentage of similarity and a similarity score.
Pros & Cons of EMBOSS:
Pros
o EMBOSS is used both for local and global alignment between sequences of the same
type
o It has a good self- explanatory GUI
o This tool has a detailed help describing every input required for comparing two
sequences
6