proteins global alignment using BLOSUM80

Question

[EE]

how an i use the BLOSUM 80 or 62 to make protein global alignment from which module should i import BLOSUM 80 or 62 and how can i use it

Answer 1

[Andrzej Zielezinski]

You can use web server or standalone tool, named needle from EMBOSS. Needle performs global alignment between two sequences. You can select the substitution matrix (BLOSUM62, BLOSUM80, and many more).

If you are on Linux (Debian/Ubuntu) you can install the tool from the repositories.

sudo apt-get install emboss

Write your protein sequences in FASTA to two files.

seq1.fasta

>seq1
MKSTGHKIWER

seq2.fasta

>seq2
MKSTSHKIWGR

You can run needle from the command line. You only need to specify the two input FASTA files (-asequence and -bsequence), output file (-outfile) and scoring system to generate the global alignments, by default: -gapopen 10 (the gap open penalty is the score taken away when a gap is created, -gapextend 0.5 (the gap extension, penalty is added to the standard gap penalty for each base or residue in the gap, and substitution matrix BLOSUM62.

needle -asequence seq1.fasta -bsequence seq2.fasta -outfile output.txt -gapopen 10 -gapextend 0.5

You can change the substitution matrix to BLOSUM80.

needle -asequence seq1.fasta -bsequence seq2.fasta -outfile output.txt -gapopen 10 -gapextend 0.5 -datafile /usr/share/EMBOSS/data/EBLOSUM80

You will get the alignment in output.txt.

########################################
# Program: needle
# Rundate: Sat 18 Dec 2021 14:38:58
# Commandline: needle
#    -asequence seq1.fasta
#    -bsequence seq2.fasta
#    -outfile output.txt
#    -gapopen 10
#    -gapextend 0.5
#    -datafile /usr/share/EMBOSS/data/EBLOSUM80
# Align_format: srspair
# Report_file: output.txt
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: seq1
# 2: seq2
# Matrix: /usr/share/EMBOSS/data/EBLOSUM80
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 11
# Identity:       9/11 (81.8%)
# Similarity:     9/11 (81.8%)
# Gaps:           0/11 ( 0.0%)
# Score: 79.0
# 
#
#=======================================

seq1               1 MKSTGHKIWER     11
                     ||||.||||.|
seq2               1 MKSTSHKIWGR     11


#---------------------------------------
#---------------------------------------

[EE]

please can you explain what this command do in details? thanks in advance

[Andrzej Zielezinski]

I updated my answer. Let me know if you need further information.