What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

Question

I have two DNA strings:

GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC

and

AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG

I want a tool that allows me to do something like this on the command line:

$ aligner  GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG

and receive an ASCII visualization of a pairwise alignment. Something like this would work:

GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC---------
---------AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG

I prefer a tool that is packaged on bioconda. A tool that also does protein and RNA sequences is even more preferable.

Answer 1

You are looking for the needle program from the EMBOSS suite. Available in bioconda.

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needle.html

To read sequences from the commandline, you need so specify the format as asis. To get the output on the screen, you'll need -stdout and to use the default alignment parameters (gap penalty 10, extend_penalty 0.5) you'll need -auto. Thus your query above would be:

$ needle -asequence asis:GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC -bsequence asis:AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG -auto -stdout
########################################
# Program: needle
# Rundate: Tue 27 Nov 2018 10:48:50
# Commandline: needle
#    -asequence asis:GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC
#    -bsequence asis:AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG
#    -auto
#    -stdout
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 56
# Identity:      37/56 (66.1%)
# Similarity:    37/56 (66.1%)
# Gaps:          18/56 (32.1%)
# Score: 181.0
# 
#
#=======================================

asis               1 GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC---     47
                              |||||||||||||||||||||||||||||||||||||.   
asis               1 ---------AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAG     41

asis              47 ------     47

asis              42 AGGAGG     47


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

Answer 2

Install biopython with conda and use the following script:

#!/usr/bin/env python
import sys
from Bio import Align
aligner = Align.PairwiseAligner()
aligner.mode = "local"
alignments = aligner.align(sys.argv[1], sys.argv[2])
print(alignments[0])

The output is then:

.GGA-GGAGGGAG--AAGGAGGGAGGGAAGA-GGAGGGAG--AAGGAGGGAGGC
.|-|-||||||||--|||-|||-|||||-||-||||||||--|||-|||-|||.
AG-AAGGAGGGAGGGAAG-AGG-AGGGA-GAAGGAGGGAGGGAAG-AGG-AGG.

There are a LOT of alignments with that same score and you can tweak the details of the mode by changing aligner.mode.

Answer 3

I'd just use something like t_coffee and write a little bash function to run it on the strings you give:

aligner(){
  tmp=$(mktemp);
  args=("$@")
  for ((i=0; i<$#; i++)); do
    printf '>%s\n%s\n' $i ${args[i]} >> "$tmp"
  done
  t_coffee "$tmp"  2>/dev/null | /bin/grep -Pv '^CLUSTAL|^\s*$'
  rm "$tmp"

}

If you add that to your shell's initialization file (e.g. ~/.bashrc if using bash on Linux, ~/.profile if using bash on macOS), you can run align2seqs with as many sequences as you want to align:

$ aligner 'GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC' 'AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG'
0               GG--AGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC
1               nAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGG-GAAGAGGAGG
                    *********      *******  *********  * ** *  * 
$ aligner 'GAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC' 'GGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG' GAGGGAGGGAAGAGGAGGGAGAAGGATCCGAGGAAGAGGAGG AGAAGGAGGGAGGGAAGAGGCCCGAGATATATAAGGATCCGAGGAA
0               GA-GG----GAGAAGGAGGGAGGGAAGAGGAGGGAGAAGG--AGGGAGGC
1               GGAGG----GAGGGAAGAGGAGGGAGAAGGAGGGAG-GGA--AGAGGAGG
2               GA-GG----GAGGGAAGAGGAGGGAGAAGGATCCGA-GGA--AGAGGAGG
3               AGAAGGAGGGAGGGAAGAGGCCCGAGATATAT--AA-GGATCCGAG-GAA
                    *    ***      **   **     *       *    * *    

Answer 4

Here's another option: https://github.com/noporpoise/seq-align; I've used it in the past as it is small and has no dependencies (just make and you're set).