PepAln: Simple Peptide Alignment Visualization

This Python package is designed match short peptide sequences detected via Mass Spectroscopy to a FASTA file then produce alignment outputs in various formats. An input file format would be:

Peptide     F145I/Dd2Dd2    Mass_Spec_Mode
VG;GV          3.493           POS
PA             2.454           POS
SP             4.701           NEG

What does this package do?

A collaborator asked me to align short peptides from a Mass Spec experiment to a sequence, then show him an image that displays in an easy-to-see format where does each peptide align and which regions are not covered.

For example, when they had a series of short fragments like:

VL LS LSP LSPAD PA NVKAA NVK VKA AA

And an origin sequence of:

VLSPADKTNVKAAWGK

They wanted to see it matched in a way that lets them see which region is well covered and which region is not covered. I came up with the following visualization that also displays individual, non-overlapping alignments with a packing heuristic:

VLSPADKTNVKAAWG
      **      
VL PA   NVKAA  
 LS     NVK    
 LSP     VKA     
 LSPAD     AA     

The * above indicates a region that is not covered. In addition they wanted to display different peptides with colors as well.

I was unable to locate a tool that has a similar functionality, hence I wrote this package.

Installation

pip install pepaln

Usage

python -m pepaln -m fragments.txt -r reference.fa

Generates the files called output.gff, output.txt and output.pdf

Input data

The input consists of a tab delimited format with at least three columns:

Peptide     F145I/Dd2Dd2    Mass_Spec_Mode
VG;GV          3.493           POS
PA             2.454           POS
SP             4.701           NEG

Where:

1. The first column lists the peptide sequence (multiple sequences may be separated with a semicolon ;).
2. The second column lists a value
3. The third column indicates the ionization mode

The reference fasta file may contain more than one target sequence.

>ha
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPN
>hb
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHL

A separate visualization will be generated for each reference sequence.

Outputs

The tool will generate outputs in three formats TXT, GFF as well as PDF formats. The default filenames are

• output.txt, output.gff, output.pdf

You may override each.

Text output:

>ha (Mode=POS)
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPN
             **                    *   *         *                            
VL PA   NVKAA  KVGA AGEYG  AL RMF   PTT TYF HFD   GSAQV   GKKV DAL  AV      PN
 LS  DKTNVK    KVGAHA EY    LE   LS      YFPH DL    AQVKG GKKVADA TNAVAHVDDM  
 LSP     VKA    VGA  GEYGA                FPH DLS    QV     KVA AL  AVAH      
 LSPAD     AA    GAHA   GAEA               PHF LS    QVK     VA ALTNA AHV     
   PADK           AHAG                     PHFD       VKGH       LT  VA       
                   HAGEYG                   HFDL       KGHGKKVA      VAH      

PDF output

The peptides are colored by their value field:

GFF output:

ha	VL	.	1	2	.	2.433	.	Mode=POS
ha	LS	.	2	3	.	4.806	.	Mode=POS
ha	LSP	.	2	4	.	2.522	.	Mode=POS
ha	LSPAD	.	2	6	.	1.613	.	Mode=POS
ha	PA	.	4	5	.	2.2	.	Mode=POS
ha	PADK	.	4	7	.	1.548	.	Mode=POS
ha	DKTNVK	.	6	11	.	1.845	.	Mode=POS
ha	NVKAA	.	9	13	.	3.012	.	Mode=POS
ha	VKA	.	10	12	.	3.986	.	Mode=POS
...

Help

$ python -m pepaln
usage: __main__.py [-h] [-m MASS] [-r REF] [-p output.pdf] [-t output.txt]
                   [-g output.gff]

optional arguments:
  -h, --help            show this help message and exit
  -m MASS, --mass MASS  Mass-spec result file containing peptide sequences.
  -r REF, --ref REF     Reference file to match the peptides against.
  -p output.pdf, --pdf output.pdf
                        Output file for pdf file
  -t output.txt, --txt output.txt
                        Output file for text alignments
  -g output.gff, --gff output.gff
                        Output file as GFF data